Starting phenix.real_space_refine on Wed Nov 19 23:06:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.map" model { file = "/net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d04_7784/11_2025/6d04_7784.cif" } resolution = 3.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 S 142 5.16 5 C 18252 2.51 5 N 4850 2.21 5 O 5498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28748 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "B" Number of atoms: 5081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5081 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 615} Chain: "C" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "D" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5266 Classifications: {'peptide': 679} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 29, 'TRANS': 644} Chain: "E" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "F" Number of atoms: 3904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3904 Classifications: {'peptide': 466} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 457} Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 24 Unusual residues: {' FE': 2, 'CO3': 2, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.13, per 1000 atoms: 0.25 Number of scatterers: 28748 At special positions: 0 Unit cell: (168.75, 148.5, 166.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 142 16.00 O 5498 8.00 N 4850 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 363 " distance=2.04 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 363 " distance=2.04 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 48 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 137 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 158 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 179 " distance=2.02 Simple disulfide: pdb=" SG CYS C 171 " - pdb=" SG CYS C 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 227 " - pdb=" SG CYS C 241 " distance=2.02 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 596 " distance=2.02 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 377 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 368 " distance=2.03 Simple disulfide: pdb=" SG CYS C 402 " - pdb=" SG CYS C 674 " distance=2.03 Simple disulfide: pdb=" SG CYS C 418 " - pdb=" SG CYS C 637 " distance=2.03 Simple disulfide: pdb=" SG CYS C 450 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 665 " distance=2.03 Simple disulfide: pdb=" SG CYS C 484 " - pdb=" SG CYS C 498 " distance=2.03 Simple disulfide: pdb=" SG CYS C 495 " - pdb=" SG CYS C 506 " distance=2.02 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 48 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 118 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 137 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 158 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 179 " distance=2.02 Simple disulfide: pdb=" SG CYS D 171 " - pdb=" SG CYS D 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 227 " - pdb=" SG CYS D 241 " distance=2.02 Simple disulfide: pdb=" SG CYS D 339 " - pdb=" SG CYS D 596 " distance=2.02 Simple disulfide: pdb=" SG CYS D 345 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 368 " distance=2.03 Simple disulfide: pdb=" SG CYS D 402 " - pdb=" SG CYS D 674 " distance=2.03 Simple disulfide: pdb=" SG CYS D 418 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS D 450 " - pdb=" SG CYS D 523 " distance=2.03 Simple disulfide: pdb=" SG CYS D 474 " - pdb=" SG CYS D 665 " distance=2.03 Simple disulfide: pdb=" SG CYS D 484 " - pdb=" SG CYS D 498 " distance=2.03 Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 506 " distance=2.02 Simple disulfide: pdb=" SG CYS D 563 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 615 " - pdb=" SG CYS D 620 " distance=2.03 Simple disulfide: pdb=" SG CYS E 240 " - pdb=" SG CYS E 284 " distance=2.03 Simple disulfide: pdb=" SG CYS E 312 " - pdb=" SG CYS E 316 " distance=2.04 Simple disulfide: pdb=" SG CYS F 240 " - pdb=" SG CYS F 284 " distance=2.03 Simple disulfide: pdb=" SG CYS F 312 " - pdb=" SG CYS F 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 802 " - " ASN A 251 " " NAG B 802 " - " ASN B 251 " " NAG C 707 " - " ASN C 611 " " NAG D 707 " - " ASN D 611 " " NAG G 1 " - " ASN A 317 " " NAG H 1 " - " ASN A 727 " " NAG I 1 " - " ASN B 317 " " NAG J 1 " - " ASN B 727 " " NAG K 1 " - " ASN C 413 " " NAG L 1 " - " ASN D 413 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 28 sheets defined 50.2% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 123 through 136 removed outlier: 4.034A pdb=" N ARG A 129 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 147 removed outlier: 4.322A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 176 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.655A pdb=" N LYS A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 439 removed outlier: 3.573A pdb=" N THR A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.628A pdb=" N THR A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.620A pdb=" N SER A 530 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 583 through 603 Processing helix chain 'A' and resid 610 through 612 No H-bonds generated for 'chain 'A' and resid 610 through 612' Processing helix chain 'A' and resid 613 through 627 removed outlier: 3.679A pdb=" N GLN A 617 " --> pdb=" O ARG A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 635 Processing helix chain 'A' and resid 639 through 662 removed outlier: 3.595A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 681 removed outlier: 3.537A pdb=" N LYS A 673 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 674 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG A 677 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 686 Processing helix chain 'A' and resid 708 through 721 removed outlier: 4.125A pdb=" N LEU A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 720 " --> pdb=" O LEU A 716 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 750 removed outlier: 3.665A pdb=" N PHE A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 750 " --> pdb=" O ALA A 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 136 removed outlier: 4.034A pdb=" N ARG B 129 " --> pdb=" O ASP B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 removed outlier: 4.322A pdb=" N THR B 143 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 176 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 263 through 274 Processing helix chain 'B' and resid 338 through 347 removed outlier: 3.654A pdb=" N LYS B 344 " --> pdb=" O ALA B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 439 removed outlier: 3.572A pdb=" N THR B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 removed outlier: 3.629A pdb=" N THR B 464 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 527 through 531 removed outlier: 3.620A pdb=" N SER B 530 " --> pdb=" O ASN B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 573 through 580 Processing helix chain 'B' and resid 583 through 603 Processing helix chain 'B' and resid 610 through 612 No H-bonds generated for 'chain 'B' and resid 610 through 612' Processing helix chain 'B' and resid 613 through 627 removed outlier: 3.678A pdb=" N GLN B 617 " --> pdb=" O ARG B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 635 Processing helix chain 'B' and resid 639 through 662 removed outlier: 3.595A pdb=" N TYR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 681 removed outlier: 3.538A pdb=" N LYS B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 674 " --> pdb=" O VAL B 670 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG B 677 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 686 Processing helix chain 'B' and resid 708 through 721 removed outlier: 4.125A pdb=" N LEU B 718 " --> pdb=" O GLU B 714 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 750 removed outlier: 3.664A pdb=" N PHE B 731 " --> pdb=" O ASN B 727 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 29 removed outlier: 3.959A pdb=" N SER C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL C 29 " --> pdb=" O HIS C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.570A pdb=" N CYS C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 68 Processing helix chain 'C' and resid 128 through 136 removed outlier: 3.569A pdb=" N LEU C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 139 No H-bonds generated for 'chain 'C' and resid 137 through 139' Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.582A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 216 through 223 removed outlier: 3.884A pdb=" N TYR C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 275 removed outlier: 3.615A pdb=" N ILE C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 275 " --> pdb=" O GLN C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 316 through 329 removed outlier: 3.574A pdb=" N VAL C 320 " --> pdb=" O GLY C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.519A pdb=" N ALA C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 403 removed outlier: 3.808A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 472 removed outlier: 3.711A pdb=" N LEU C 466 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 496 removed outlier: 3.552A pdb=" N CYS C 495 " --> pdb=" O SER C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 527 removed outlier: 3.513A pdb=" N GLY C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 520 " --> pdb=" O GLY C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 548 through 553 removed outlier: 3.631A pdb=" N LYS C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 548 through 553' Processing helix chain 'C' and resid 593 through 609 removed outlier: 4.026A pdb=" N LEU C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 652 removed outlier: 3.658A pdb=" N GLY C 652 " --> pdb=" O GLU C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 668 through 676 removed outlier: 3.626A pdb=" N GLU C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 29 removed outlier: 3.959A pdb=" N SER D 28 " --> pdb=" O ASP D 24 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL D 29 " --> pdb=" O HIS D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.570A pdb=" N CYS D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 Processing helix chain 'D' and resid 128 through 136 removed outlier: 3.569A pdb=" N LEU D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.582A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 197 Processing helix chain 'D' and resid 208 through 214 Processing helix chain 'D' and resid 216 through 223 removed outlier: 3.884A pdb=" N TYR D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 275 removed outlier: 3.616A pdb=" N ILE D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D 273 " --> pdb=" O GLN D 269 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY D 275 " --> pdb=" O GLN D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.575A pdb=" N VAL D 320 " --> pdb=" O GLY D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 362 Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.519A pdb=" N ALA D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 403 removed outlier: 3.807A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 472 removed outlier: 3.711A pdb=" N LEU D 466 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.552A pdb=" N CYS D 495 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 527 removed outlier: 3.513A pdb=" N GLY D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D 520 " --> pdb=" O GLY D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 548 through 553 removed outlier: 3.630A pdb=" N LYS D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN D 553 " --> pdb=" O PRO D 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 548 through 553' Processing helix chain 'D' and resid 593 through 609 removed outlier: 4.025A pdb=" N LEU D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 652 removed outlier: 3.657A pdb=" N GLY D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 668 through 676 removed outlier: 3.625A pdb=" N GLU D 672 " --> pdb=" O SER D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 212 removed outlier: 4.349A pdb=" N TYR E 200 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 240 Processing helix chain 'E' and resid 240 through 255 Processing helix chain 'E' and resid 266 through 308 removed outlier: 3.816A pdb=" N LYS E 270 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS E 288 " --> pdb=" O CYS E 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 335 removed outlier: 4.569A pdb=" N LYS E 326 " --> pdb=" O PHE E 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET E 335 " --> pdb=" O ASP E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 362 removed outlier: 3.594A pdb=" N LYS E 360 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 406 Processing helix chain 'E' and resid 415 through 477 removed outlier: 3.620A pdb=" N GLU E 460 " --> pdb=" O ASN E 456 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLY E 463 " --> pdb=" O GLY E 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS E 464 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG E 468 " --> pdb=" O HIS E 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP E 474 " --> pdb=" O SER E 470 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR E 477 " --> pdb=" O ILE E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 510 removed outlier: 5.466A pdb=" N LYS E 505 " --> pdb=" O ASP E 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 512 No H-bonds generated for 'chain 'E' and resid 511 through 512' Processing helix chain 'E' and resid 513 through 517 removed outlier: 3.967A pdb=" N LEU E 516 " --> pdb=" O TYR E 513 " (cutoff:3.500A) Processing helix chain 'E' and resid 519 through 566 removed outlier: 4.035A pdb=" N ASP E 524 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL E 560 " --> pdb=" O GLU E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 590 removed outlier: 3.792A pdb=" N ASP E 578 " --> pdb=" O GLN E 574 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 633 removed outlier: 3.716A pdb=" N ILE E 633 " --> pdb=" O VAL E 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 212 removed outlier: 4.348A pdb=" N TYR F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 240 Processing helix chain 'F' and resid 240 through 255 Processing helix chain 'F' and resid 266 through 308 removed outlier: 3.816A pdb=" N LYS F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS F 288 " --> pdb=" O CYS F 284 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LYS F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 335 removed outlier: 4.569A pdb=" N LYS F 326 " --> pdb=" O PHE F 322 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET F 335 " --> pdb=" O ASP F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 362 removed outlier: 3.594A pdb=" N LYS F 360 " --> pdb=" O ASP F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 406 Processing helix chain 'F' and resid 415 through 477 removed outlier: 3.620A pdb=" N GLU F 460 " --> pdb=" O ASN F 456 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY F 463 " --> pdb=" O GLY F 459 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU F 467 " --> pdb=" O GLY F 463 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG F 468 " --> pdb=" O HIS F 464 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP F 474 " --> pdb=" O SER F 470 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR F 477 " --> pdb=" O ILE F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 510 removed outlier: 5.466A pdb=" N LYS F 505 " --> pdb=" O ASP F 501 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 511 through 512 No H-bonds generated for 'chain 'F' and resid 511 through 512' Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.967A pdb=" N LEU F 516 " --> pdb=" O TYR F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 566 removed outlier: 4.034A pdb=" N ASP F 524 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 574 through 590 removed outlier: 3.791A pdb=" N ASP F 578 " --> pdb=" O GLN F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 633 removed outlier: 3.715A pdb=" N ILE F 633 " --> pdb=" O VAL F 629 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 193 removed outlier: 4.118A pdb=" N SER A 447 " --> pdb=" O PRO A 399 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS A 401 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 449 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 403 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA A 451 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL A 405 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP A 453 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA A 407 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA A 478 " --> pdb=" O ASP A 400 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR A 402 " --> pdb=" O ALA A 478 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR A 480 " --> pdb=" O TYR A 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY A 406 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE A 555 " --> pdb=" O ASN A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 214 removed outlier: 7.389A pdb=" N VAL A 200 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 352 removed outlier: 6.778A pdb=" N ASP A 352 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG A 364 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 193 removed outlier: 4.119A pdb=" N SER B 447 " --> pdb=" O PRO B 399 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HIS B 401 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 449 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 403 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA B 451 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B 405 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TRP B 453 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 407 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA B 478 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B 402 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR B 480 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 406 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 555 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 210 through 214 removed outlier: 7.390A pdb=" N VAL B 200 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AA9, first strand: chain 'B' and resid 232 through 234 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 removed outlier: 6.778A pdb=" N ASP B 352 " --> pdb=" O ARG B 364 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 364 " --> pdb=" O ASP B 352 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 60 through 62 removed outlier: 3.932A pdb=" N VAL C 60 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 251 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA C 99 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 226 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER C 117 " --> pdb=" O CYS C 158 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 244 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 342 through 347 removed outlier: 6.060A pdb=" N VAL C 342 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL C 369 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TRP C 344 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ALA C 371 " --> pdb=" O TRP C 344 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA C 346 " --> pdb=" O ALA C 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 388 through 391 removed outlier: 6.429A pdb=" N VAL C 587 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 483 through 484 removed outlier: 7.210A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 450 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS C 534 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA C 430 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 562 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 569 " --> pdb=" O LEU C 561 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 483 through 484 removed outlier: 7.210A pdb=" N SER C 449 " --> pdb=" O CYS C 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS C 450 " --> pdb=" O PHE C 532 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS C 534 " --> pdb=" O CYS C 450 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AC2, first strand: chain 'D' and resid 60 through 62 removed outlier: 3.933A pdb=" N VAL D 60 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 251 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA D 99 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 226 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 157 through 158 removed outlier: 6.818A pdb=" N SER D 117 " --> pdb=" O CYS D 158 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 244 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 342 through 347 removed outlier: 6.059A pdb=" N VAL D 342 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D 369 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TRP D 344 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 371 " --> pdb=" O TRP D 344 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA D 346 " --> pdb=" O ALA D 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 388 through 391 removed outlier: 6.428A pdb=" N VAL D 587 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.209A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS D 450 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS D 534 " --> pdb=" O CYS D 450 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA D 430 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 562 " --> pdb=" O ALA D 430 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS D 569 " --> pdb=" O LEU D 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 483 through 484 removed outlier: 7.209A pdb=" N SER D 449 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N CYS D 450 " --> pdb=" O PHE D 532 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N LYS D 534 " --> pdb=" O CYS D 450 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 180 through 181 removed outlier: 4.082A pdb=" N ILE E 180 " --> pdb=" O ILE E 189 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 180 through 181 removed outlier: 4.082A pdb=" N ILE F 180 " --> pdb=" O ILE F 189 " (cutoff:3.500A) 1434 hydrogen bonds defined for protein. 4194 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: 6.50 Time building geometry restraints manager: 3.34 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: 8531 1.34 - 1.46: 6384 1.46 - 1.58: 14253 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 29360 Sorted by residual: bond pdb=" CA ARG B 155 " pdb=" CB ARG B 155 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.46e-02 4.69e+03 7.32e+00 bond pdb=" CA ARG A 155 " pdb=" CB ARG A 155 " ideal model delta sigma weight residual 1.524 1.563 -0.039 1.46e-02 4.69e+03 7.13e+00 bond pdb=" C1 NAG C 707 " pdb=" O5 NAG C 707 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" N ASN B 236 " pdb=" CA ASN B 236 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.79e+00 bond pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.71e+00 ... (remaining 29355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 38540 2.78 - 5.56: 1000 5.56 - 8.34: 92 8.34 - 11.12: 24 11.12 - 13.89: 8 Bond angle restraints: 39664 Sorted by residual: angle pdb=" CA TYR E 422 " pdb=" CB TYR E 422 " pdb=" CG TYR E 422 " ideal model delta sigma weight residual 113.90 127.79 -13.89 1.80e+00 3.09e-01 5.96e+01 angle pdb=" CA TYR F 422 " pdb=" CB TYR F 422 " pdb=" CG TYR F 422 " ideal model delta sigma weight residual 113.90 127.76 -13.86 1.80e+00 3.09e-01 5.93e+01 angle pdb=" C GLY C 502 " pdb=" N LEU C 503 " pdb=" CA LEU C 503 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.40e+01 angle pdb=" C GLY D 502 " pdb=" N LEU D 503 " pdb=" CA LEU D 503 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C ASN C 461 " pdb=" N ILE C 462 " pdb=" CA ILE C 462 " ideal model delta sigma weight residual 120.24 123.28 -3.04 6.30e-01 2.52e+00 2.32e+01 ... (remaining 39659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 17249 21.89 - 43.78: 632 43.78 - 65.67: 109 65.67 - 87.56: 32 87.56 - 109.46: 20 Dihedral angle restraints: 18042 sinusoidal: 7570 harmonic: 10472 Sorted by residual: dihedral pdb=" CA GLN F 317 " pdb=" C GLN F 317 " pdb=" N THR F 318 " pdb=" CA THR F 318 " ideal model delta harmonic sigma weight residual 180.00 92.36 87.64 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA GLN E 317 " pdb=" C GLN E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 92.41 87.59 0 5.00e+00 4.00e-02 3.07e+02 dihedral pdb=" CA ASP F 407 " pdb=" C ASP F 407 " pdb=" N GLY F 408 " pdb=" CA GLY F 408 " ideal model delta harmonic sigma weight residual -180.00 -93.39 -86.61 0 5.00e+00 4.00e-02 3.00e+02 ... (remaining 18039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 4324 0.187 - 0.374: 22 0.374 - 0.561: 4 0.561 - 0.748: 2 0.748 - 0.934: 2 Chirality restraints: 4354 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 727 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 727 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 251 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 4351 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 422 " 0.049 2.00e-02 2.50e+03 3.04e-02 1.85e+01 pdb=" CG TYR F 422 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 422 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 422 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR F 422 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 422 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR F 422 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 422 " -0.049 2.00e-02 2.50e+03 3.03e-02 1.83e+01 pdb=" CG TYR E 422 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 422 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 422 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 422 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 422 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 422 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 251 " -0.035 2.00e-02 2.50e+03 3.27e-02 1.34e+01 pdb=" CG ASN B 251 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN B 251 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN B 251 " 0.037 2.00e-02 2.50e+03 pdb=" C1 NAG B 802 " -0.035 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 199 2.58 - 3.16: 22835 3.16 - 3.74: 43443 3.74 - 4.32: 59605 4.32 - 4.90: 97765 Nonbonded interactions: 223847 Sorted by model distance: nonbonded pdb="FE FE D 703 " pdb=" O3 CO3 D 704 " model vdw 2.001 2.260 nonbonded pdb="FE FE C 703 " pdb=" O3 CO3 C 704 " model vdw 2.012 2.260 nonbonded pdb=" OD1 ASP D 63 " pdb="FE FE D 703 " model vdw 2.035 2.260 nonbonded pdb=" OH TYR C 95 " pdb="FE FE C 703 " model vdw 2.039 2.260 nonbonded pdb=" OD1 ASP C 63 " pdb="FE FE C 703 " model vdw 2.043 2.260 ... (remaining 223842 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.460 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: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.160 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 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 : 0.008 0.074 29422 Z= 0.356 Angle : 1.110 21.991 39804 Z= 0.613 Chirality : 0.062 0.934 4354 Planarity : 0.007 0.071 5106 Dihedral : 12.378 109.455 11164 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.21 % Allowed : 6.30 % Favored : 92.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.11), residues: 3560 helix: -2.00 (0.10), residues: 1672 sheet: -1.14 (0.26), residues: 336 loop : -2.07 (0.13), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 208 TYR 0.069 0.003 TYR E 422 PHE 0.037 0.003 PHE A 176 TRP 0.040 0.004 TRP D 358 HIS 0.011 0.002 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00813 (29360) covalent geometry : angle 1.07309 (39664) SS BOND : bond 0.00545 ( 46) SS BOND : angle 1.86529 ( 92) hydrogen bonds : bond 0.14266 ( 1414) hydrogen bonds : angle 7.95272 ( 4194) link_BETA1-4 : bond 0.01240 ( 6) link_BETA1-4 : angle 7.76895 ( 18) link_NAG-ASN : bond 0.01844 ( 10) link_NAG-ASN : angle 8.11245 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 394 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 LEU cc_start: 0.9117 (pp) cc_final: 0.8823 (pp) REVERT: A 510 MET cc_start: 0.8501 (mtp) cc_final: 0.8251 (mtm) REVERT: A 570 MET cc_start: 0.8531 (ttm) cc_final: 0.8230 (ttm) REVERT: A 574 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7771 (pttm) REVERT: A 671 MET cc_start: 0.8622 (mmm) cc_final: 0.8290 (mmt) REVERT: B 126 ASP cc_start: 0.8253 (t70) cc_final: 0.7698 (t0) REVERT: C 309 MET cc_start: 0.8719 (ttm) cc_final: 0.8405 (mtp) REVERT: C 367 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7831 (mt-10) REVERT: C 389 MET cc_start: 0.8145 (ptm) cc_final: 0.7935 (ttp) REVERT: C 477 ASP cc_start: 0.7388 (p0) cc_final: 0.6827 (t0) REVERT: C 514 TYR cc_start: 0.7794 (m-10) cc_final: 0.7279 (m-80) REVERT: D 309 MET cc_start: 0.8835 (ttm) cc_final: 0.8456 (mtp) REVERT: D 514 TYR cc_start: 0.7757 (m-10) cc_final: 0.7307 (m-80) REVERT: E 324 MET cc_start: 0.7810 (mmm) cc_final: 0.6517 (tpp) REVERT: E 596 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6688 (tm-30) REVERT: E 608 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8599 (mm) REVERT: F 205 PHE cc_start: 0.8483 (t80) cc_final: 0.8195 (t80) REVERT: F 414 VAL cc_start: 0.6230 (m) cc_final: 0.5933 (m) REVERT: F 508 GLU cc_start: 0.7659 (tt0) cc_final: 0.7433 (tp30) REVERT: F 631 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6663 (tp30) outliers start: 38 outliers final: 4 residues processed: 428 average time/residue: 0.2096 time to fit residues: 136.5960 Evaluate side-chains 145 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain E residue 608 ILE Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN A 197 GLN A 236 ASN A 275 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 626 ASN A 640 GLN A 715 ASN B 148 ASN B 197 GLN B 236 ASN B 275 ASN B 483 ASN B 608 ASN B 626 ASN B 640 GLN B 715 ASN B 721 GLN C 55 ASN C 300 HIS C 411 ASN C 417 ASN ** C 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 GLN ** C 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 GLN C 618 ASN D 55 ASN D 300 HIS D 411 ASN D 417 ASN ** D 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN ** D 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 GLN D 618 ASN E 227 ASN E 252 ASN E 256 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN E 346 GLN E 364 GLN E 444 ASN E 456 ASN F 227 ASN F 252 ASN F 364 GLN F 444 ASN F 456 ASN F 527 ASN ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.091685 restraints weight = 54900.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.090358 restraints weight = 62699.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091603 restraints weight = 67922.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.091935 restraints weight = 41506.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092857 restraints weight = 36819.931| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29422 Z= 0.159 Angle : 0.686 17.035 39804 Z= 0.354 Chirality : 0.046 0.634 4354 Planarity : 0.005 0.058 5106 Dihedral : 8.588 84.264 4221 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 2.24 % Allowed : 9.24 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3560 helix: 0.12 (0.12), residues: 1684 sheet: -0.71 (0.28), residues: 318 loop : -1.67 (0.14), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 217 TYR 0.055 0.002 TYR F 422 PHE 0.039 0.002 PHE E 521 TRP 0.025 0.002 TRP B 740 HIS 0.008 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00338 (29360) covalent geometry : angle 0.65941 (39664) SS BOND : bond 0.00309 ( 46) SS BOND : angle 1.04123 ( 92) hydrogen bonds : bond 0.06606 ( 1414) hydrogen bonds : angle 5.25103 ( 4194) link_BETA1-4 : bond 0.00651 ( 6) link_BETA1-4 : angle 4.23928 ( 18) link_NAG-ASN : bond 0.00956 ( 10) link_NAG-ASN : angle 5.87695 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 166 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 VAL cc_start: 0.8777 (t) cc_final: 0.8546 (m) REVERT: A 364 ARG cc_start: 0.8738 (mmt-90) cc_final: 0.8486 (mmt-90) REVERT: A 432 MET cc_start: 0.7897 (mtp) cc_final: 0.7002 (ttm) REVERT: A 474 LEU cc_start: 0.9073 (pp) cc_final: 0.8746 (pp) REVERT: A 574 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8065 (pttm) REVERT: A 671 MET cc_start: 0.8616 (mmm) cc_final: 0.8253 (mmt) REVERT: B 126 ASP cc_start: 0.7597 (t70) cc_final: 0.7282 (t0) REVERT: B 624 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7837 (m-30) REVERT: C 235 VAL cc_start: 0.8994 (m) cc_final: 0.8774 (p) REVERT: C 309 MET cc_start: 0.8734 (ttm) cc_final: 0.8451 (mtp) REVERT: C 477 ASP cc_start: 0.7312 (p0) cc_final: 0.6924 (t0) REVERT: C 499 MET cc_start: 0.8184 (ptm) cc_final: 0.7875 (ptm) REVERT: C 514 TYR cc_start: 0.7787 (m-10) cc_final: 0.7277 (m-80) REVERT: D 62 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8320 (pp) REVERT: D 309 MET cc_start: 0.8753 (ttm) cc_final: 0.8399 (mtp) REVERT: D 477 ASP cc_start: 0.7246 (p0) cc_final: 0.6847 (t0) REVERT: D 499 MET cc_start: 0.8173 (ptm) cc_final: 0.7888 (ptm) REVERT: D 514 TYR cc_start: 0.7724 (m-10) cc_final: 0.7511 (m-80) REVERT: E 346 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8241 (pp30) REVERT: F 205 PHE cc_start: 0.8206 (t80) cc_final: 0.7936 (t80) REVERT: F 335 MET cc_start: 0.6254 (tmm) cc_final: 0.5894 (tpt) outliers start: 70 outliers final: 32 residues processed: 226 average time/residue: 0.1765 time to fit residues: 65.3528 Evaluate side-chains 148 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 371 LYS Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 574 LYS Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 470 SER Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 572 ASN Chi-restraints excluded: chain F residue 632 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 193 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 87 optimal weight: 0.0970 chunk 116 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 721 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 628 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.091984 restraints weight = 54695.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.090550 restraints weight = 64801.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091999 restraints weight = 66549.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092190 restraints weight = 41779.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.093438 restraints weight = 37273.541| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 29422 Z= 0.140 Angle : 0.629 15.054 39804 Z= 0.319 Chirality : 0.044 0.563 4354 Planarity : 0.004 0.045 5106 Dihedral : 7.346 72.521 4215 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.24 % Allowed : 10.45 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3560 helix: 1.01 (0.12), residues: 1672 sheet: -0.63 (0.29), residues: 320 loop : -1.34 (0.14), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.045 0.001 TYR F 422 PHE 0.026 0.001 PHE F 521 TRP 0.021 0.001 TRP B 740 HIS 0.004 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00295 (29360) covalent geometry : angle 0.60188 (39664) SS BOND : bond 0.00485 ( 46) SS BOND : angle 1.39867 ( 92) hydrogen bonds : bond 0.05974 ( 1414) hydrogen bonds : angle 4.84621 ( 4194) link_BETA1-4 : bond 0.01137 ( 6) link_BETA1-4 : angle 4.39213 ( 18) link_NAG-ASN : bond 0.00817 ( 10) link_NAG-ASN : angle 5.26036 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8003 (mtp) cc_final: 0.7018 (ttm) REVERT: A 474 LEU cc_start: 0.9088 (pp) cc_final: 0.8730 (pp) REVERT: A 671 MET cc_start: 0.8684 (mmm) cc_final: 0.8375 (mmt) REVERT: B 126 ASP cc_start: 0.7500 (t70) cc_final: 0.7138 (t0) REVERT: B 147 LEU cc_start: 0.9078 (mt) cc_final: 0.8874 (mm) REVERT: B 624 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: C 62 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8232 (pp) REVERT: C 235 VAL cc_start: 0.9032 (m) cc_final: 0.8800 (p) REVERT: C 309 MET cc_start: 0.8718 (ttm) cc_final: 0.8417 (mtp) REVERT: C 477 ASP cc_start: 0.7206 (p0) cc_final: 0.6813 (t0) REVERT: C 499 MET cc_start: 0.8277 (ptm) cc_final: 0.7865 (ptm) REVERT: C 514 TYR cc_start: 0.7894 (m-10) cc_final: 0.7301 (m-80) REVERT: D 62 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8282 (pp) REVERT: D 309 MET cc_start: 0.8681 (ttm) cc_final: 0.8343 (mtp) REVERT: D 477 ASP cc_start: 0.7165 (p0) cc_final: 0.6910 (t0) REVERT: D 499 MET cc_start: 0.8355 (ptm) cc_final: 0.8032 (ptm) REVERT: D 514 TYR cc_start: 0.7876 (m-10) cc_final: 0.7358 (m-80) REVERT: E 223 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7380 (mmmt) REVERT: E 279 GLU cc_start: 0.7759 (mp0) cc_final: 0.6929 (mp0) REVERT: E 422 TYR cc_start: 0.7581 (OUTLIER) cc_final: 0.5885 (t80) REVERT: F 205 PHE cc_start: 0.8028 (t80) cc_final: 0.7592 (t80) REVERT: F 335 MET cc_start: 0.6184 (tmm) cc_final: 0.5644 (tpt) REVERT: F 422 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7859 (m-80) outliers start: 70 outliers final: 31 residues processed: 193 average time/residue: 0.1724 time to fit residues: 55.6701 Evaluate side-chains 143 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 292 ASN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 3 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 301 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS C 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN E 397 HIS F 252 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.085965 restraints weight = 54866.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.084450 restraints weight = 60253.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.085455 restraints weight = 67352.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.086097 restraints weight = 39420.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087625 restraints weight = 34273.410| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 29422 Z= 0.252 Angle : 0.710 13.767 39804 Z= 0.365 Chirality : 0.048 0.555 4354 Planarity : 0.004 0.041 5106 Dihedral : 6.874 70.462 4211 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 11.13 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3560 helix: 1.26 (0.12), residues: 1698 sheet: -0.75 (0.27), residues: 348 loop : -1.30 (0.15), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 680 TYR 0.040 0.002 TYR E 218 PHE 0.023 0.002 PHE C 22 TRP 0.025 0.002 TRP B 740 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00592 (29360) covalent geometry : angle 0.68629 (39664) SS BOND : bond 0.00493 ( 46) SS BOND : angle 1.73020 ( 92) hydrogen bonds : bond 0.06442 ( 1414) hydrogen bonds : angle 4.87723 ( 4194) link_BETA1-4 : bond 0.00843 ( 6) link_BETA1-4 : angle 4.57368 ( 18) link_NAG-ASN : bond 0.01003 ( 10) link_NAG-ASN : angle 5.02762 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 121 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8222 (mtm) cc_final: 0.7297 (ttm) REVERT: A 671 MET cc_start: 0.8916 (mmm) cc_final: 0.8654 (mmt) REVERT: B 126 ASP cc_start: 0.7823 (t70) cc_final: 0.7516 (t0) REVERT: B 364 ARG cc_start: 0.8932 (mmt-90) cc_final: 0.8408 (mmt-90) REVERT: B 476 LEU cc_start: 0.9346 (mm) cc_final: 0.9138 (mt) REVERT: C 62 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8394 (pp) REVERT: C 112 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8782 (tm) REVERT: C 309 MET cc_start: 0.8751 (ttm) cc_final: 0.8463 (mtp) REVERT: C 477 ASP cc_start: 0.7339 (p0) cc_final: 0.6765 (t0) REVERT: C 514 TYR cc_start: 0.7974 (m-10) cc_final: 0.7580 (m-80) REVERT: C 540 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8779 (mp10) REVERT: D 62 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8458 (pp) REVERT: D 309 MET cc_start: 0.8713 (ttm) cc_final: 0.8315 (mtp) REVERT: D 477 ASP cc_start: 0.7354 (p0) cc_final: 0.6751 (t0) REVERT: D 499 MET cc_start: 0.8431 (ptm) cc_final: 0.8149 (ptm) REVERT: D 514 TYR cc_start: 0.7959 (m-10) cc_final: 0.7573 (m-80) REVERT: E 205 PHE cc_start: 0.8049 (t80) cc_final: 0.7663 (t80) REVERT: E 223 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7588 (mmmt) REVERT: E 352 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8851 (mt) REVERT: E 357 MET cc_start: 0.7487 (mmm) cc_final: 0.7175 (mmt) REVERT: E 422 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.6515 (t80) REVERT: F 205 PHE cc_start: 0.8186 (t80) cc_final: 0.7619 (t80) REVERT: F 324 MET cc_start: 0.6556 (OUTLIER) cc_final: 0.5976 (mpm) REVERT: F 335 MET cc_start: 0.6082 (tmm) cc_final: 0.5572 (tpt) REVERT: F 352 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8961 (mt) REVERT: F 357 MET cc_start: 0.7625 (tpt) cc_final: 0.7413 (mmt) REVERT: F 422 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7313 (m-80) outliers start: 87 outliers final: 46 residues processed: 199 average time/residue: 0.1734 time to fit residues: 57.5542 Evaluate side-chains 158 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 228 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 329 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 212 HIS ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.115236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088370 restraints weight = 54613.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.087804 restraints weight = 68134.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.088575 restraints weight = 72376.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.089169 restraints weight = 42484.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090368 restraints weight = 36600.195| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29422 Z= 0.152 Angle : 0.624 14.744 39804 Z= 0.319 Chirality : 0.044 0.639 4354 Planarity : 0.003 0.039 5106 Dihedral : 6.655 69.385 4210 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.46 % Allowed : 11.96 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.14), residues: 3560 helix: 1.61 (0.12), residues: 1694 sheet: -0.60 (0.29), residues: 324 loop : -1.14 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.040 0.001 TYR E 218 PHE 0.016 0.001 PHE C 22 TRP 0.019 0.001 TRP B 740 HIS 0.003 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00341 (29360) covalent geometry : angle 0.59882 (39664) SS BOND : bond 0.00274 ( 46) SS BOND : angle 1.60466 ( 92) hydrogen bonds : bond 0.05829 ( 1414) hydrogen bonds : angle 4.64206 ( 4194) link_BETA1-4 : bond 0.00686 ( 6) link_BETA1-4 : angle 4.30783 ( 18) link_NAG-ASN : bond 0.00777 ( 10) link_NAG-ASN : angle 4.86843 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 110 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8245 (mtm) cc_final: 0.7380 (ttm) REVERT: A 671 MET cc_start: 0.8854 (mmm) cc_final: 0.8554 (mmt) REVERT: B 126 ASP cc_start: 0.7659 (t70) cc_final: 0.7380 (t0) REVERT: C 62 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8255 (pp) REVERT: C 112 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8735 (tm) REVERT: C 309 MET cc_start: 0.8705 (ttm) cc_final: 0.8397 (mtp) REVERT: C 477 ASP cc_start: 0.7177 (p0) cc_final: 0.6762 (t0) REVERT: C 514 TYR cc_start: 0.7987 (m-10) cc_final: 0.7307 (m-80) REVERT: C 643 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7453 (p0) REVERT: D 62 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8289 (pp) REVERT: D 112 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8933 (tm) REVERT: D 309 MET cc_start: 0.8659 (ttm) cc_final: 0.8353 (mtp) REVERT: D 477 ASP cc_start: 0.7216 (p0) cc_final: 0.6756 (t0) REVERT: D 499 MET cc_start: 0.8396 (ptm) cc_final: 0.8028 (ptm) REVERT: D 514 TYR cc_start: 0.7964 (m-10) cc_final: 0.7324 (m-80) REVERT: E 205 PHE cc_start: 0.7919 (t80) cc_final: 0.7434 (t80) REVERT: E 263 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7650 (tm-30) REVERT: E 346 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8162 (pp30) REVERT: E 357 MET cc_start: 0.7310 (mmm) cc_final: 0.6922 (mmm) REVERT: E 422 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.6402 (t80) REVERT: F 205 PHE cc_start: 0.7778 (t80) cc_final: 0.7275 (t80) REVERT: F 335 MET cc_start: 0.6137 (tmm) cc_final: 0.5662 (tpt) REVERT: F 422 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7228 (m-80) outliers start: 77 outliers final: 42 residues processed: 181 average time/residue: 0.1669 time to fit residues: 50.8603 Evaluate side-chains 155 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 104 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 188 optimal weight: 6.9990 chunk 233 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 252 optimal weight: 0.3980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 684 HIS C 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.115172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087927 restraints weight = 54673.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.087070 restraints weight = 64376.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.087844 restraints weight = 72816.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088539 restraints weight = 41894.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089624 restraints weight = 35621.931| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29422 Z= 0.157 Angle : 0.617 14.128 39804 Z= 0.313 Chirality : 0.044 0.573 4354 Planarity : 0.003 0.039 5106 Dihedral : 6.478 68.254 4210 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.69 % Allowed : 12.15 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3560 helix: 1.79 (0.12), residues: 1694 sheet: -0.58 (0.29), residues: 324 loop : -1.05 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 364 TYR 0.032 0.001 TYR F 422 PHE 0.017 0.001 PHE C 22 TRP 0.019 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00353 (29360) covalent geometry : angle 0.59341 (39664) SS BOND : bond 0.00331 ( 46) SS BOND : angle 1.39950 ( 92) hydrogen bonds : bond 0.05663 ( 1414) hydrogen bonds : angle 4.51729 ( 4194) link_BETA1-4 : bond 0.00783 ( 6) link_BETA1-4 : angle 4.36241 ( 18) link_NAG-ASN : bond 0.00809 ( 10) link_NAG-ASN : angle 4.78124 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 112 time to evaluate : 1.057 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 432 MET cc_start: 0.8271 (mtm) cc_final: 0.7408 (ttm) REVERT: A 474 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 671 MET cc_start: 0.8928 (mmm) cc_final: 0.8683 (mmt) REVERT: A 672 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8372 (ttmt) REVERT: B 126 ASP cc_start: 0.7640 (t70) cc_final: 0.7367 (t0) REVERT: B 364 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8106 (mmt180) REVERT: C 62 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8277 (pp) REVERT: C 112 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8772 (tm) REVERT: C 309 MET cc_start: 0.8674 (ttm) cc_final: 0.8405 (mtp) REVERT: C 514 TYR cc_start: 0.8020 (m-10) cc_final: 0.7348 (m-80) REVERT: D 62 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8295 (pp) REVERT: D 112 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8947 (tm) REVERT: D 309 MET cc_start: 0.8530 (ttm) cc_final: 0.8221 (mtp) REVERT: D 499 MET cc_start: 0.8421 (ptm) cc_final: 0.8061 (ptm) REVERT: D 514 TYR cc_start: 0.8046 (m-10) cc_final: 0.7382 (m-80) REVERT: E 205 PHE cc_start: 0.7992 (t80) cc_final: 0.7565 (t80) REVERT: E 263 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: E 352 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8839 (mt) REVERT: E 357 MET cc_start: 0.7513 (mmm) cc_final: 0.7040 (mmm) REVERT: E 422 TYR cc_start: 0.7664 (OUTLIER) cc_final: 0.6527 (t80) REVERT: F 205 PHE cc_start: 0.8023 (t80) cc_final: 0.7445 (t80) REVERT: F 263 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: F 335 MET cc_start: 0.6195 (tmm) cc_final: 0.5685 (tpt) REVERT: F 422 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7203 (m-80) outliers start: 84 outliers final: 52 residues processed: 191 average time/residue: 0.1633 time to fit residues: 53.1894 Evaluate side-chains 164 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 101 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 240 CYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 292 ASN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 216 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 56 optimal weight: 0.0010 chunk 212 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 301 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS B 148 ASN B 640 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 212 HIS ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 626 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.089260 restraints weight = 54350.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088393 restraints weight = 65896.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089383 restraints weight = 70698.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.089706 restraints weight = 42526.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091966 restraints weight = 37295.119| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29422 Z= 0.129 Angle : 0.607 19.426 39804 Z= 0.306 Chirality : 0.044 0.709 4354 Planarity : 0.003 0.039 5106 Dihedral : 6.314 66.420 4210 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.43 % Allowed : 12.76 % Favored : 84.81 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.14), residues: 3560 helix: 1.95 (0.12), residues: 1694 sheet: -0.51 (0.30), residues: 320 loop : -0.99 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 364 TYR 0.034 0.001 TYR E 218 PHE 0.014 0.001 PHE C 22 TRP 0.017 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00277 (29360) covalent geometry : angle 0.58013 (39664) SS BOND : bond 0.00325 ( 46) SS BOND : angle 1.54652 ( 92) hydrogen bonds : bond 0.05453 ( 1414) hydrogen bonds : angle 4.42050 ( 4194) link_BETA1-4 : bond 0.00634 ( 6) link_BETA1-4 : angle 4.41454 ( 18) link_NAG-ASN : bond 0.01003 ( 10) link_NAG-ASN : angle 5.03206 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 110 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8447 (m-40) REVERT: A 432 MET cc_start: 0.8208 (mtm) cc_final: 0.7435 (ttm) REVERT: A 671 MET cc_start: 0.8952 (mmm) cc_final: 0.8651 (mmt) REVERT: A 672 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8359 (ttmt) REVERT: B 126 ASP cc_start: 0.7656 (t70) cc_final: 0.7406 (t0) REVERT: C 62 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8210 (pp) REVERT: C 112 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8766 (tm) REVERT: C 309 MET cc_start: 0.8674 (ttm) cc_final: 0.8379 (mtp) REVERT: C 514 TYR cc_start: 0.8065 (m-10) cc_final: 0.7309 (m-80) REVERT: D 26 MET cc_start: 0.9343 (tpp) cc_final: 0.8826 (tpp) REVERT: D 62 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8232 (pp) REVERT: D 309 MET cc_start: 0.8507 (ttm) cc_final: 0.8217 (mtp) REVERT: D 499 MET cc_start: 0.8387 (ptm) cc_final: 0.7995 (ptm) REVERT: D 514 TYR cc_start: 0.8047 (m-10) cc_final: 0.7397 (m-80) REVERT: E 205 PHE cc_start: 0.7983 (t80) cc_final: 0.7489 (t80) REVERT: E 263 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: E 352 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8819 (mt) REVERT: E 357 MET cc_start: 0.7520 (mmm) cc_final: 0.7032 (mmm) REVERT: E 422 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.6495 (t80) REVERT: F 205 PHE cc_start: 0.7945 (t80) cc_final: 0.7329 (t80) REVERT: F 263 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: F 335 MET cc_start: 0.6167 (tmm) cc_final: 0.5653 (tpt) REVERT: F 422 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7152 (m-80) outliers start: 76 outliers final: 50 residues processed: 180 average time/residue: 0.1599 time to fit residues: 48.7476 Evaluate side-chains 156 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 96 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 132 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 248 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 229 optimal weight: 0.0870 chunk 187 optimal weight: 0.9980 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.117417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.089948 restraints weight = 54658.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088753 restraints weight = 64644.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.089740 restraints weight = 72022.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090399 restraints weight = 41901.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.091348 restraints weight = 36557.746| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29422 Z= 0.121 Angle : 0.592 18.815 39804 Z= 0.296 Chirality : 0.043 0.558 4354 Planarity : 0.003 0.064 5106 Dihedral : 6.177 64.256 4210 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 13.14 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.14), residues: 3560 helix: 2.08 (0.12), residues: 1694 sheet: -0.46 (0.30), residues: 320 loop : -0.93 (0.15), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 533 TYR 0.032 0.001 TYR F 218 PHE 0.015 0.001 PHE C 22 TRP 0.016 0.001 TRP B 740 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00252 (29360) covalent geometry : angle 0.56751 (39664) SS BOND : bond 0.00328 ( 46) SS BOND : angle 1.50625 ( 92) hydrogen bonds : bond 0.05244 ( 1414) hydrogen bonds : angle 4.32023 ( 4194) link_BETA1-4 : bond 0.00665 ( 6) link_BETA1-4 : angle 4.15874 ( 18) link_NAG-ASN : bond 0.00871 ( 10) link_NAG-ASN : angle 4.71706 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 109 time to evaluate : 1.137 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 432 MET cc_start: 0.8245 (mtm) cc_final: 0.7531 (ttm) REVERT: A 671 MET cc_start: 0.8965 (mmm) cc_final: 0.8682 (mmt) REVERT: A 672 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8330 (ttmt) REVERT: B 126 ASP cc_start: 0.7578 (t70) cc_final: 0.7342 (t0) REVERT: B 365 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8420 (mmm) REVERT: C 62 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8161 (pp) REVERT: C 112 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8779 (tm) REVERT: C 309 MET cc_start: 0.8642 (ttm) cc_final: 0.8369 (mtp) REVERT: C 514 TYR cc_start: 0.8109 (m-10) cc_final: 0.7357 (m-80) REVERT: D 62 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8591 (pp) REVERT: D 309 MET cc_start: 0.8652 (ttm) cc_final: 0.8208 (mtp) REVERT: D 354 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8390 (tttm) REVERT: D 499 MET cc_start: 0.8354 (ptm) cc_final: 0.7976 (ptm) REVERT: D 514 TYR cc_start: 0.8052 (m-10) cc_final: 0.7405 (m-80) REVERT: E 205 PHE cc_start: 0.8018 (t80) cc_final: 0.7518 (t80) REVERT: E 263 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: E 346 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8207 (pp30) REVERT: E 352 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8828 (mt) REVERT: E 357 MET cc_start: 0.7556 (mmm) cc_final: 0.7068 (mmm) REVERT: E 422 TYR cc_start: 0.7309 (OUTLIER) cc_final: 0.6429 (t80) REVERT: F 205 PHE cc_start: 0.7751 (t80) cc_final: 0.7255 (t80) REVERT: F 263 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: F 335 MET cc_start: 0.6211 (tmm) cc_final: 0.5676 (tpt) REVERT: F 422 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.6948 (m-80) REVERT: F 517 GLU cc_start: 0.3826 (OUTLIER) cc_final: 0.3470 (pm20) outliers start: 67 outliers final: 50 residues processed: 171 average time/residue: 0.1607 time to fit residues: 47.2284 Evaluate side-chains 158 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 95 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 125 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 365 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 235 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 221 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN E 346 GLN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087998 restraints weight = 54372.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087091 restraints weight = 63150.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.088083 restraints weight = 67137.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088788 restraints weight = 39761.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089570 restraints weight = 34767.572| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29422 Z= 0.147 Angle : 0.602 18.104 39804 Z= 0.302 Chirality : 0.043 0.500 4354 Planarity : 0.003 0.052 5106 Dihedral : 6.112 62.960 4210 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.21 % Allowed : 13.20 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.14), residues: 3560 helix: 2.08 (0.12), residues: 1694 sheet: -0.44 (0.30), residues: 328 loop : -0.92 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 232 TYR 0.025 0.001 TYR E 218 PHE 0.017 0.001 PHE D 22 TRP 0.018 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00331 (29360) covalent geometry : angle 0.57949 (39664) SS BOND : bond 0.00355 ( 46) SS BOND : angle 1.47912 ( 92) hydrogen bonds : bond 0.05318 ( 1414) hydrogen bonds : angle 4.35161 ( 4194) link_BETA1-4 : bond 0.00620 ( 6) link_BETA1-4 : angle 4.09991 ( 18) link_NAG-ASN : bond 0.00820 ( 10) link_NAG-ASN : angle 4.48677 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 102 time to evaluate : 1.063 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 432 MET cc_start: 0.8252 (mtm) cc_final: 0.7496 (ttm) REVERT: A 474 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8770 (pp) REVERT: A 671 MET cc_start: 0.9006 (mmm) cc_final: 0.8753 (mmt) REVERT: A 672 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8383 (ttmt) REVERT: B 126 ASP cc_start: 0.7710 (t70) cc_final: 0.7452 (t0) REVERT: B 365 MET cc_start: 0.8568 (mmt) cc_final: 0.8344 (mmm) REVERT: C 62 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8216 (pp) REVERT: C 112 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8811 (tm) REVERT: C 309 MET cc_start: 0.8564 (ttm) cc_final: 0.8324 (mtp) REVERT: C 514 TYR cc_start: 0.8156 (m-10) cc_final: 0.7342 (m-80) REVERT: D 62 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8241 (pp) REVERT: D 309 MET cc_start: 0.8652 (ttm) cc_final: 0.8209 (mtp) REVERT: D 354 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8442 (tttm) REVERT: D 499 MET cc_start: 0.8401 (ptm) cc_final: 0.8025 (ptm) REVERT: D 514 TYR cc_start: 0.8132 (m-10) cc_final: 0.7587 (m-10) REVERT: E 205 PHE cc_start: 0.7991 (t80) cc_final: 0.7639 (t80) REVERT: E 263 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7616 (tm-30) REVERT: E 346 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8325 (pp30) REVERT: E 352 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8842 (mt) REVERT: E 357 MET cc_start: 0.7602 (mmm) cc_final: 0.7101 (mmm) REVERT: E 422 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6321 (t80) REVERT: F 205 PHE cc_start: 0.7722 (t80) cc_final: 0.7187 (t80) REVERT: F 263 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7587 (tm-30) REVERT: F 422 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.6972 (m-80) REVERT: F 517 GLU cc_start: 0.3931 (OUTLIER) cc_final: 0.3569 (pm20) outliers start: 69 outliers final: 51 residues processed: 167 average time/residue: 0.1614 time to fit residues: 46.1902 Evaluate side-chains 157 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 93 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 240 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 517 GLU Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 206 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 302 optimal weight: 4.9990 chunk 288 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 312 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 328 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN C 451 HIS E 292 ASN E 346 GLN E 566 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.114986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.087804 restraints weight = 54785.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086845 restraints weight = 69066.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088001 restraints weight = 71888.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.088426 restraints weight = 43199.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.089783 restraints weight = 38013.923| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 29422 Z= 0.187 Angle : 0.634 17.651 39804 Z= 0.321 Chirality : 0.044 0.467 4354 Planarity : 0.003 0.047 5106 Dihedral : 6.135 62.802 4210 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.21 % Allowed : 13.46 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3560 helix: 2.02 (0.12), residues: 1696 sheet: -0.54 (0.29), residues: 348 loop : -0.93 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.028 0.001 TYR F 525 PHE 0.020 0.002 PHE D 22 TRP 0.018 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00435 (29360) covalent geometry : angle 0.61298 (39664) SS BOND : bond 0.00411 ( 46) SS BOND : angle 1.54093 ( 92) hydrogen bonds : bond 0.05556 ( 1414) hydrogen bonds : angle 4.44798 ( 4194) link_BETA1-4 : bond 0.00581 ( 6) link_BETA1-4 : angle 4.10474 ( 18) link_NAG-ASN : bond 0.00781 ( 10) link_NAG-ASN : angle 4.38991 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7120 Ramachandran restraints generated. 3560 Oldfield, 0 Emsley, 3560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 94 time to evaluate : 1.206 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 432 MET cc_start: 0.8271 (mtm) cc_final: 0.7505 (ttm) REVERT: A 474 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8749 (pp) REVERT: A 671 MET cc_start: 0.9050 (mmm) cc_final: 0.8789 (mmt) REVERT: A 672 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8350 (ttmt) REVERT: B 126 ASP cc_start: 0.7797 (t70) cc_final: 0.7500 (t0) REVERT: B 364 ARG cc_start: 0.7861 (mmp80) cc_final: 0.7527 (mmt-90) REVERT: C 62 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8295 (pp) REVERT: C 112 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8803 (tm) REVERT: C 309 MET cc_start: 0.8672 (ttm) cc_final: 0.8379 (mtp) REVERT: C 514 TYR cc_start: 0.8126 (m-10) cc_final: 0.7342 (m-80) REVERT: D 62 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8303 (pp) REVERT: D 309 MET cc_start: 0.8683 (ttm) cc_final: 0.8320 (mtp) REVERT: D 354 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8441 (tttm) REVERT: D 499 MET cc_start: 0.8461 (ptm) cc_final: 0.8077 (ptm) REVERT: D 514 TYR cc_start: 0.8099 (m-10) cc_final: 0.7543 (m-10) REVERT: E 205 PHE cc_start: 0.7701 (t80) cc_final: 0.7426 (t80) REVERT: E 263 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: E 346 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8347 (pp30) REVERT: E 352 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8854 (mt) REVERT: E 357 MET cc_start: 0.7605 (mmm) cc_final: 0.7186 (mmm) REVERT: E 422 TYR cc_start: 0.7188 (OUTLIER) cc_final: 0.6436 (t80) REVERT: F 205 PHE cc_start: 0.7620 (t80) cc_final: 0.7158 (t80) REVERT: F 263 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: F 335 MET cc_start: 0.6642 (tpt) cc_final: 0.6331 (tpp) REVERT: F 422 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6955 (m-80) outliers start: 69 outliers final: 52 residues processed: 158 average time/residue: 0.1633 time to fit residues: 44.3756 Evaluate side-chains 158 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 94 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 660 PHE Chi-restraints excluded: chain A residue 672 LYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 603 HIS Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 259 LYS Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 354 LYS Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 538 VAL Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 222 HIS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 409 VAL Chi-restraints excluded: chain E residue 422 TYR Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 501 ASP Chi-restraints excluded: chain E residue 521 PHE Chi-restraints excluded: chain E residue 572 ASN Chi-restraints excluded: chain E residue 632 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 GLU Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 422 TYR Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Chi-restraints excluded: chain F residue 572 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 260 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 chunk 339 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 182 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 347 optimal weight: 4.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 451 HIS E 346 GLN E 566 ASN ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086301 restraints weight = 53876.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.085056 restraints weight = 95617.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.086170 restraints weight = 79604.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087732 restraints weight = 47789.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088032 restraints weight = 36289.071| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29422 Z= 0.205 Angle : 0.649 17.387 39804 Z= 0.330 Chirality : 0.045 0.454 4354 Planarity : 0.004 0.043 5106 Dihedral : 6.174 63.251 4210 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.17 % Allowed : 13.43 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3560 helix: 1.97 (0.12), residues: 1692 sheet: -0.63 (0.28), residues: 364 loop : -0.97 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.028 0.002 TYR F 525 PHE 0.021 0.002 PHE C 22 TRP 0.018 0.002 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00481 (29360) covalent geometry : angle 0.62919 (39664) SS BOND : bond 0.00437 ( 46) SS BOND : angle 1.57269 ( 92) hydrogen bonds : bond 0.05699 ( 1414) hydrogen bonds : angle 4.52452 ( 4194) link_BETA1-4 : bond 0.00571 ( 6) link_BETA1-4 : angle 4.05488 ( 18) link_NAG-ASN : bond 0.00771 ( 10) link_NAG-ASN : angle 4.33393 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3495.69 seconds wall clock time: 62 minutes 4.44 seconds (3724.44 seconds total)