Starting phenix.real_space_refine on Mon Sep 14 05:31:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_7784.cif Found real_map, /net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_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_7784/09_2026/6d04_7784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_7784.map" model { file = "/net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_7784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_7784.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_7784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6d04_7784/09_2026/6d04_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 7.19, 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: 2.65 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: 0.80 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: 5.43 Time building geometry restraints manager: 3.55 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 - 17.64: 16685 17.64 - 35.28: 780 35.28 - 52.92: 191 52.92 - 70.56: 18 70.56 - 88.19: 32 Dihedral angle restraints: 17706 sinusoidal: 7234 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 17703 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.330 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 11.438 87.644 10828 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/Z covalent geometry : bond 0.00813 / 0.36 (29360) covalent geometry : angle 1.07309 / 0.61 (39664) SS BOND : bond 0.00545 / 0.33 ( 46) SS BOND : angle 1.86529 / 1.30 ( 92) hydrogen bonds : bond 0.14266 / 9.31 ( 1414) hydrogen bonds : angle 7.95272 / 5.52 ( 4194) link_BETA1-4 : bond 0.01240 / 0.67 ( 6) link_BETA1-4 : angle 7.76895 / 4.40 ( 18) link_NAG-ASN : bond 0.01844 / 0.89 ( 10) link_NAG-ASN : angle 8.11245 / 5.40 ( 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 : 1.164 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: 0.7772 (pttm) REVERT: A 671 MET cc_start: 0.8622 (mmm) cc_final: 0.8290 (mmt) REVERT: B 126 ASP cc_start: 0.8254 (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: 0.7934 (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: 0.7366 (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: 0.7306 (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: 0.5934 (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: 0.2191 time to fit residues: 144.3378 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 : 1.109 ------------------------------------------------------------------------------- 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... 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 256 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: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091804 restraints weight = 54920.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.090976 restraints weight = 63648.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092111 restraints weight = 66010.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092378 restraints weight = 41297.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093371 restraints weight = 36594.503| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29422 Z= 0.160 Angle : 0.685 17.243 39804 Z= 0.355 Chirality : 0.045 0.565 4354 Planarity : 0.005 0.055 5106 Dihedral : 6.136 73.137 3885 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.55 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: -1.10 (0.13), residues: 3560 helix: 0.10 (0.12), residues: 1696 sheet: -0.70 (0.28), residues: 318 loop : -1.65 (0.14), residues: 1546 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 0.026 0.002 TRP B 740 HIS 0.008 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (29360) covalent geometry : angle 0.66009 / 0.35 (39664) SS BOND : bond 0.00286 / 0.18 ( 46) SS BOND : angle 1.11369 / 0.79 ( 92) hydrogen bonds : bond 0.06571 / 4.39 ( 1414) hydrogen bonds : angle 5.21892 / 3.61 ( 4194) link_BETA1-4 : bond 0.00855 / 0.54 ( 6) link_BETA1-4 : angle 4.04011 / 2.31 ( 18) link_NAG-ASN : bond 0.00979 / 0.51 ( 10) link_NAG-ASN : angle 5.75634 / 3.99 ( 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 239 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 169 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.7887 (mtp) cc_final: 0.7018 (ttm) REVERT: A 474 LEU cc_start: 0.9064 (pp) cc_final: 0.8744 (pp) REVERT: A 574 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8018 (pttm) REVERT: A 671 MET cc_start: 0.8615 (mmm) cc_final: 0.8247 (mmt) REVERT: B 126 ASP cc_start: 0.7575 (t70) cc_final: 0.7268 (t0) REVERT: B 624 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: C 235 VAL cc_start: 0.9000 (m) cc_final: 0.8778 (p) REVERT: C 309 MET cc_start: 0.8726 (ttm) cc_final: 0.8456 (mtp) REVERT: C 477 ASP cc_start: 0.7248 (p0) cc_final: 0.6910 (t0) REVERT: C 499 MET cc_start: 0.8142 (ptm) cc_final: 0.7847 (ptm) REVERT: C 514 TYR cc_start: 0.7783 (m-10) cc_final: 0.7281 (m-80) REVERT: D 62 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8308 (pp) REVERT: D 309 MET cc_start: 0.8753 (ttm) cc_final: 0.8390 (mtp) REVERT: D 477 ASP cc_start: 0.7188 (p0) cc_final: 0.6839 (t0) REVERT: D 499 MET cc_start: 0.8164 (ptm) cc_final: 0.7891 (ptm) REVERT: D 514 TYR cc_start: 0.7723 (m-10) cc_final: 0.7517 (m-80) REVERT: E 279 GLU cc_start: 0.7437 (mp0) cc_final: 0.7086 (mp0) REVERT: E 346 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: F 205 PHE cc_start: 0.8061 (t80) cc_final: 0.7832 (t80) REVERT: F 335 MET cc_start: 0.6144 (tmm) cc_final: 0.5821 (tpt) outliers start: 70 outliers final: 31 residues processed: 228 average time/residue: 0.1821 time to fit residues: 67.9145 Evaluate side-chains 147 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 285 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 87 optimal weight: 0.4980 chunk 116 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 206 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN B 721 GLN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093076 restraints weight = 54561.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.092021 restraints weight = 61636.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092924 restraints weight = 68782.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093295 restraints weight = 42846.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093682 restraints weight = 36835.058| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 0.049 29422 Z= 0.129 Angle : 0.615 14.943 39804 Z= 0.313 Chirality : 0.043 0.505 4354 Planarity : 0.004 0.052 5106 Dihedral : 5.602 72.669 3879 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.27 % Allowed : 10.55 % Favored : 87.18 % 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: 1.00 (0.12), residues: 1676 sheet: -0.64 (0.29), residues: 320 loop : -1.34 (0.14), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 220 TYR 0.044 0.001 TYR F 422 PHE 0.028 0.001 PHE F 521 TRP 0.019 0.001 TRP B 740 HIS 0.004 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (29360) covalent geometry : angle 0.58897 / 0.31 (39664) SS BOND : bond 0.00694 / 0.39 ( 46) SS BOND : angle 1.43253 / 0.95 ( 92) hydrogen bonds : bond 0.05863 / 3.93 ( 1414) hydrogen bonds : angle 4.80194 / 3.31 ( 4194) link_BETA1-4 : bond 0.00762 / 0.38 ( 6) link_BETA1-4 : angle 4.10573 / 2.34 ( 18) link_NAG-ASN : bond 0.00881 / 0.45 ( 10) link_NAG-ASN : angle 5.10369 / 3.50 ( 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 205 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 134 time to evaluate : 1.175 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: 0.7924 (mtp) cc_final: 0.6982 (ttm) REVERT: A 474 LEU cc_start: 0.9032 (pp) cc_final: 0.8702 (pp) REVERT: A 671 MET cc_start: 0.8647 (mmm) cc_final: 0.8315 (mmt) REVERT: B 126 ASP cc_start: 0.7416 (t70) cc_final: 0.7039 (t0) REVERT: B 364 ARG cc_start: 0.8448 (mmt180) cc_final: 0.8076 (mmt-90) REVERT: B 624 ASP cc_start: 0.8152 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: C 62 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8202 (pp) REVERT: C 235 VAL cc_start: 0.9024 (m) cc_final: 0.8791 (p) REVERT: C 309 MET cc_start: 0.8719 (ttm) cc_final: 0.8415 (mtp) REVERT: C 477 ASP cc_start: 0.7497 (p0) cc_final: 0.7072 (t0) REVERT: C 499 MET cc_start: 0.8234 (ptm) cc_final: 0.7985 (ptm) REVERT: C 514 TYR cc_start: 0.7951 (m-10) cc_final: 0.7337 (m-80) REVERT: D 267 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8954 (mp) REVERT: D 309 MET cc_start: 0.8679 (ttm) cc_final: 0.8341 (mtp) REVERT: D 477 ASP cc_start: 0.7444 (p0) cc_final: 0.7166 (t0) REVERT: D 499 MET cc_start: 0.8180 (ptm) cc_final: 0.7883 (ptm) REVERT: D 514 TYR cc_start: 0.7875 (m-10) cc_final: 0.7375 (m-80) REVERT: E 223 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7601 (mmmt) REVERT: E 279 GLU cc_start: 0.7747 (mp0) cc_final: 0.7010 (mp0) REVERT: E 422 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.5882 (t80) REVERT: E 601 MET cc_start: 0.8315 (mmm) cc_final: 0.7356 (mmt) REVERT: F 205 PHE cc_start: 0.8029 (t80) cc_final: 0.7557 (t80) REVERT: F 335 MET cc_start: 0.6163 (tmm) cc_final: 0.5639 (tpt) outliers start: 71 outliers final: 27 residues processed: 194 average time/residue: 0.1745 time to fit residues: 57.0472 Evaluate side-chains 144 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 371 LYS 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 723 ASN Chi-restraints excluded: chain B residue 122 LEU 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 611 ASN Chi-restraints excluded: chain C residue 643 ASP Chi-restraints excluded: chain D residue 259 LYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 643 ASP Chi-restraints excluded: chain E residue 223 LYS Chi-restraints excluded: chain E residue 292 ASN 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 365 ILE 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: 1.9990 chunk 338 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 159 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 250 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087235 restraints weight = 55141.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.086302 restraints weight = 68282.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.086955 restraints weight = 77373.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087531 restraints weight = 45702.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089314 restraints weight = 38240.086| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29422 Z= 0.215 Angle : 0.675 13.762 39804 Z= 0.347 Chirality : 0.047 0.590 4354 Planarity : 0.004 0.057 5106 Dihedral : 5.425 70.425 3875 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.72 % Allowed : 10.97 % Favored : 86.32 % 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: 0.10 (0.14), residues: 3560 helix: 1.36 (0.12), residues: 1696 sheet: -0.57 (0.29), residues: 312 loop : -1.28 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 680 TYR 0.040 0.002 TYR E 218 PHE 0.022 0.002 PHE C 22 TRP 0.027 0.002 TRP B 740 HIS 0.005 0.001 HIS B 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (29360) covalent geometry : angle 0.65363 / 0.34 (39664) SS BOND : bond 0.00703 / 0.34 ( 46) SS BOND : angle 1.64101 / 1.18 ( 92) hydrogen bonds : bond 0.06229 / 4.15 ( 1414) hydrogen bonds : angle 4.76624 / 3.30 ( 4194) link_BETA1-4 : bond 0.00707 / 0.37 ( 6) link_BETA1-4 : angle 3.84090 / 2.18 ( 18) link_NAG-ASN : bond 0.00744 / 0.36 ( 10) link_NAG-ASN : angle 4.74946 / 3.34 ( 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 209 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 124 time to evaluate : 1.167 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: 0.8291 (mtm) cc_final: 0.7284 (ttm) REVERT: A 671 MET cc_start: 0.8955 (mmm) cc_final: 0.8689 (mmt) REVERT: B 126 ASP cc_start: 0.7737 (t70) cc_final: 0.7452 (t0) REVERT: B 679 MET cc_start: 0.8841 (mtt) cc_final: 0.8568 (mtm) REVERT: C 62 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8367 (pp) REVERT: C 112 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8736 (tm) REVERT: C 235 VAL cc_start: 0.9088 (m) cc_final: 0.8880 (p) REVERT: C 309 MET cc_start: 0.8726 (ttm) cc_final: 0.8445 (mtp) REVERT: C 477 ASP cc_start: 0.7313 (p0) cc_final: 0.6776 (t0) REVERT: C 499 MET cc_start: 0.8449 (ptm) cc_final: 0.8178 (ptm) REVERT: C 514 TYR cc_start: 0.8013 (m-10) cc_final: 0.7347 (m-80) REVERT: C 540 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8768 (mp10) REVERT: D 62 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8462 (pp) REVERT: D 309 MET cc_start: 0.8694 (ttm) cc_final: 0.8293 (mtp) REVERT: D 477 ASP cc_start: 0.7292 (p0) cc_final: 0.6739 (t0) REVERT: D 514 TYR cc_start: 0.7955 (m-10) cc_final: 0.7363 (m-80) REVERT: E 205 PHE cc_start: 0.7972 (t80) cc_final: 0.7600 (t80) REVERT: E 223 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7590 (mmmt) REVERT: E 357 MET cc_start: 0.7535 (mmm) cc_final: 0.7260 (mmt) REVERT: E 422 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6511 (t80) REVERT: F 205 PHE cc_start: 0.8141 (t80) cc_final: 0.7569 (t80) REVERT: F 324 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5974 (mpm) REVERT: F 335 MET cc_start: 0.6204 (tmm) cc_final: 0.5697 (tpt) outliers start: 85 outliers final: 45 residues processed: 201 average time/residue: 0.1741 time to fit residues: 59.3898 Evaluate side-chains 159 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 1.225 ------------------------------------------------------------------------------- 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 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 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 262 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 GLU 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 540 GLN Chi-restraints excluded: chain C residue 611 ASN 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 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 240 CYS 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 292 ASN Chi-restraints excluded: chain F residue 324 MET Chi-restraints excluded: chain F residue 365 ILE Chi-restraints excluded: chain F residue 415 THR 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: 0.0030 chunk 51 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 336 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 310 optimal weight: 9.9990 chunk 81 optimal weight: 0.2980 chunk 299 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 overall best weight: 1.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089176 restraints weight = 54553.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.088504 restraints weight = 65598.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.089239 restraints weight = 71457.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.089979 restraints weight = 43890.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.090670 restraints weight = 37881.633| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29422 Z= 0.141 Angle : 0.614 17.108 39804 Z= 0.315 Chirality : 0.044 0.626 4354 Planarity : 0.003 0.038 5106 Dihedral : 5.245 69.331 3874 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.30 % Allowed : 11.76 % Favored : 85.93 % 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: 0.46 (0.14), residues: 3560 helix: 1.70 (0.12), residues: 1692 sheet: -0.57 (0.29), residues: 320 loop : -1.11 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 207 TYR 0.041 0.001 TYR E 218 PHE 0.016 0.001 PHE D 84 TRP 0.017 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (29360) covalent geometry : angle 0.59065 / 0.31 (39664) SS BOND : bond 0.00285 / 0.17 ( 46) SS BOND : angle 1.89234 / 1.09 ( 92) hydrogen bonds : bond 0.05694 / 3.79 ( 1414) hydrogen bonds : angle 4.54655 / 3.17 ( 4194) link_BETA1-4 : bond 0.00539 / 0.29 ( 6) link_BETA1-4 : angle 3.72448 / 2.11 ( 18) link_NAG-ASN : bond 0.00726 / 0.37 ( 10) link_NAG-ASN : angle 4.49103 / 3.02 ( 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 192 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 120 time to evaluate : 1.142 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: 0.8184 (mtm) cc_final: 0.7316 (ttm) REVERT: A 671 MET cc_start: 0.8798 (mmm) cc_final: 0.8548 (mmt) REVERT: B 126 ASP cc_start: 0.7577 (t70) cc_final: 0.7319 (t0) REVERT: B 364 ARG cc_start: 0.8849 (mmt-90) cc_final: 0.8441 (mmt-90) REVERT: B 679 MET cc_start: 0.8783 (mtt) cc_final: 0.8490 (mtm) REVERT: C 62 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8209 (pp) REVERT: C 112 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8720 (tm) REVERT: C 309 MET cc_start: 0.8645 (ttm) cc_final: 0.8363 (mtp) REVERT: C 477 ASP cc_start: 0.7515 (p0) cc_final: 0.7053 (t0) REVERT: C 499 MET cc_start: 0.8248 (ptm) cc_final: 0.7900 (ptm) REVERT: C 514 TYR cc_start: 0.8001 (m-10) cc_final: 0.7363 (m-80) REVERT: D 62 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8278 (pp) REVERT: D 112 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (tm) REVERT: D 309 MET cc_start: 0.8673 (ttm) cc_final: 0.8430 (mtp) REVERT: D 477 ASP cc_start: 0.7561 (p0) cc_final: 0.7111 (t0) REVERT: D 499 MET cc_start: 0.8219 (ptm) cc_final: 0.7877 (ptm) REVERT: D 514 TYR cc_start: 0.7975 (m-10) cc_final: 0.7372 (m-80) REVERT: D 540 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8762 (mp10) REVERT: E 205 PHE cc_start: 0.7971 (t80) cc_final: 0.7390 (t80) REVERT: E 263 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: E 422 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6428 (t80) REVERT: F 205 PHE cc_start: 0.7775 (t80) cc_final: 0.7242 (t80) REVERT: F 335 MET cc_start: 0.6116 (tmm) cc_final: 0.5649 (tpt) outliers start: 72 outliers final: 37 residues processed: 184 average time/residue: 0.1620 time to fit residues: 51.0352 Evaluate side-chains 153 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 362 THR Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 566 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 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 611 ASN 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 540 GLN 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 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 365 ILE Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 560 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 188 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 245 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 684 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3548 r_free = 0.3548 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087089 restraints weight = 54412.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.086604 restraints weight = 65489.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.087436 restraints weight = 66536.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.088053 restraints weight = 39611.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.089189 restraints weight = 34317.547| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29422 Z= 0.176 Angle : 0.619 12.683 39804 Z= 0.317 Chirality : 0.045 0.582 4354 Planarity : 0.003 0.037 5106 Dihedral : 5.141 68.360 3874 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.40 % Allowed : 12.47 % Favored : 85.13 % 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: 0.60 (0.14), residues: 3560 helix: 1.83 (0.12), residues: 1694 sheet: -0.55 (0.29), residues: 324 loop : -1.04 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 623 TYR 0.031 0.001 TYR F 218 PHE 0.019 0.002 PHE C 22 TRP 0.021 0.001 TRP B 740 HIS 0.005 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (29360) covalent geometry : angle 0.59880 / 0.31 (39664) SS BOND : bond 0.00454 / 0.25 ( 46) SS BOND : angle 1.40890 / 0.95 ( 92) hydrogen bonds : bond 0.05707 / 3.81 ( 1414) hydrogen bonds : angle 4.50568 / 3.13 ( 4194) link_BETA1-4 : bond 0.00679 / 0.36 ( 6) link_BETA1-4 : angle 3.51477 / 1.99 ( 18) link_NAG-ASN : bond 0.00983 / 0.46 ( 10) link_NAG-ASN : angle 4.47201 / 3.15 ( 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 190 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 115 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8253 (mtm) cc_final: 0.7416 (ttm) REVERT: A 671 MET cc_start: 0.8966 (mmm) cc_final: 0.8654 (mmt) REVERT: B 126 ASP cc_start: 0.7702 (t70) cc_final: 0.7423 (t0) REVERT: B 679 MET cc_start: 0.8859 (mtt) cc_final: 0.8577 (mtm) REVERT: C 62 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8290 (pp) REVERT: C 112 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8748 (tm) REVERT: C 309 MET cc_start: 0.8651 (ttm) cc_final: 0.8345 (mtp) REVERT: C 499 MET cc_start: 0.8359 (ptm) cc_final: 0.7981 (ptm) REVERT: C 514 TYR cc_start: 0.8072 (m-10) cc_final: 0.7362 (m-80) REVERT: D 62 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8322 (pp) REVERT: D 112 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8919 (tm) REVERT: D 309 MET cc_start: 0.8710 (ttm) cc_final: 0.8258 (mtp) REVERT: D 499 MET cc_start: 0.8349 (ptm) cc_final: 0.7966 (ptm) REVERT: D 514 TYR cc_start: 0.8040 (m-10) cc_final: 0.7371 (m-80) REVERT: D 540 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8770 (mp10) REVERT: E 205 PHE cc_start: 0.7972 (t80) cc_final: 0.7570 (t80) REVERT: E 263 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: E 352 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8839 (mt) REVERT: E 357 MET cc_start: 0.7429 (mmm) cc_final: 0.7155 (mmt) REVERT: E 422 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6483 (t80) REVERT: F 205 PHE cc_start: 0.7814 (t80) cc_final: 0.7293 (t80) REVERT: F 263 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: F 335 MET cc_start: 0.6184 (tmm) cc_final: 0.5665 (tpt) outliers start: 75 outliers final: 45 residues processed: 186 average time/residue: 0.1669 time to fit residues: 52.8107 Evaluate side-chains 155 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 101 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 561 THR Chi-restraints excluded: chain A residue 566 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 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 538 VAL Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 611 ASN 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 538 VAL Chi-restraints excluded: chain D residue 540 GLN 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 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 263 GLN Chi-restraints excluded: chain F residue 365 ILE 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: 0.7980 chunk 196 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 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: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 HIS ** E 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088374 restraints weight = 53951.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087433 restraints weight = 60113.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088257 restraints weight = 67221.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.088854 restraints weight = 41505.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.090124 restraints weight = 35563.016| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29422 Z= 0.138 Angle : 0.599 17.240 39804 Z= 0.304 Chirality : 0.044 0.569 4354 Planarity : 0.003 0.039 5106 Dihedral : 5.008 66.509 3874 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.33 % Allowed : 13.08 % Favored : 84.59 % Cbeta Deviations : 0.00 % 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: 0.74 (0.14), residues: 3560 helix: 1.95 (0.12), residues: 1694 sheet: -0.48 (0.30), residues: 324 loop : -0.97 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 533 TYR 0.046 0.001 TYR F 525 PHE 0.016 0.001 PHE C 22 TRP 0.016 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (29360) covalent geometry : angle 0.57687 / 0.30 (39664) SS BOND : bond 0.00425 / 0.22 ( 46) SS BOND : angle 1.52062 / 0.85 ( 92) hydrogen bonds : bond 0.05433 / 3.63 ( 1414) hydrogen bonds : angle 4.40144 / 3.07 ( 4194) link_BETA1-4 : bond 0.00673 / 0.36 ( 6) link_BETA1-4 : angle 3.58431 / 2.03 ( 18) link_NAG-ASN : bond 0.00911 / 0.46 ( 10) link_NAG-ASN : angle 4.67698 / 3.12 ( 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 187 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 114 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8218 (mtm) cc_final: 0.7477 (ttm) REVERT: A 671 MET cc_start: 0.8966 (mmm) cc_final: 0.8709 (mmt) REVERT: B 126 ASP cc_start: 0.7717 (t70) cc_final: 0.7449 (t0) REVERT: B 679 MET cc_start: 0.8855 (mtt) cc_final: 0.8553 (mtm) REVERT: C 62 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8199 (pp) REVERT: C 112 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8754 (tm) REVERT: C 309 MET cc_start: 0.8611 (ttm) cc_final: 0.8390 (mtp) REVERT: C 499 MET cc_start: 0.8367 (ptm) cc_final: 0.7998 (ptm) REVERT: C 514 TYR cc_start: 0.8075 (m-10) cc_final: 0.7369 (m-80) REVERT: D 62 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8250 (pp) REVERT: D 112 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8922 (tm) REVERT: D 309 MET cc_start: 0.8673 (ttm) cc_final: 0.8325 (mtp) REVERT: D 499 MET cc_start: 0.8348 (ptm) cc_final: 0.7972 (ptm) REVERT: D 514 TYR cc_start: 0.8025 (m-10) cc_final: 0.7331 (m-80) REVERT: D 540 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8764 (mp10) REVERT: E 205 PHE cc_start: 0.8039 (t80) cc_final: 0.7642 (t80) REVERT: E 263 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7630 (tm-30) REVERT: E 352 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8862 (mt) REVERT: E 357 MET cc_start: 0.7383 (mmm) cc_final: 0.7097 (mmt) REVERT: E 422 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6521 (t80) REVERT: F 205 PHE cc_start: 0.7848 (t80) cc_final: 0.7352 (t80) REVERT: F 263 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: F 335 MET cc_start: 0.6254 (tmm) cc_final: 0.5717 (tpt) outliers start: 73 outliers final: 47 residues processed: 183 average time/residue: 0.1594 time to fit residues: 50.1666 Evaluate side-chains 156 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 100 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 566 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 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 538 VAL Chi-restraints excluded: chain C residue 611 ASN 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 538 VAL Chi-restraints excluded: chain D residue 540 GLN 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 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 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 263 GLN Chi-restraints excluded: chain F residue 365 ILE 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: 2.9990 chunk 48 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 GLN D 451 HIS E 289 ASN ** F 289 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 = 0.3531 r_free = 0.3531 target = 0.113328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.086165 restraints weight = 54757.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.084712 restraints weight = 61717.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085913 restraints weight = 68167.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086336 restraints weight = 40483.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087887 restraints weight = 35513.190| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 29422 Z= 0.200 Angle : 0.632 13.205 39804 Z= 0.324 Chirality : 0.045 0.471 4354 Planarity : 0.004 0.040 5106 Dihedral : 5.049 65.888 3874 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.08 % Allowed : 13.49 % Favored : 84.43 % 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: 0.71 (0.14), residues: 3560 helix: 1.92 (0.12), residues: 1700 sheet: -0.59 (0.28), residues: 348 loop : -0.97 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.064 0.002 TYR F 525 PHE 0.021 0.002 PHE C 22 TRP 0.021 0.002 TRP B 740 HIS 0.005 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (29360) covalent geometry : angle 0.61594 / 0.32 (39664) SS BOND : bond 0.00435 / 0.27 ( 46) SS BOND : angle 1.22546 / 0.87 ( 92) hydrogen bonds : bond 0.05720 / 3.81 ( 1414) hydrogen bonds : angle 4.50584 / 3.12 ( 4194) link_BETA1-4 : bond 0.00596 / 0.32 ( 6) link_BETA1-4 : angle 3.17605 / 1.79 ( 18) link_NAG-ASN : bond 0.00712 / 0.35 ( 10) link_NAG-ASN : angle 4.28755 / 2.85 ( 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 168 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 103 time to evaluate : 1.096 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: 0.8259 (mtm) cc_final: 0.7523 (ttm) REVERT: A 474 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8783 (pp) REVERT: A 671 MET cc_start: 0.9062 (mmm) cc_final: 0.8790 (mmt) REVERT: B 126 ASP cc_start: 0.7895 (t70) cc_final: 0.7580 (t0) REVERT: B 365 MET cc_start: 0.8440 (mmt) cc_final: 0.8234 (mmm) REVERT: B 679 MET cc_start: 0.8862 (mtt) cc_final: 0.8588 (mtm) REVERT: C 62 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8358 (pp) REVERT: C 112 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8783 (tm) REVERT: C 309 MET cc_start: 0.8657 (ttm) cc_final: 0.8394 (mtp) REVERT: C 499 MET cc_start: 0.8441 (ptm) cc_final: 0.8072 (ptm) REVERT: C 514 TYR cc_start: 0.8113 (m-10) cc_final: 0.7365 (m-80) REVERT: D 62 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8385 (pp) REVERT: D 112 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8924 (tm) REVERT: D 309 MET cc_start: 0.8711 (ttm) cc_final: 0.8328 (mtp) REVERT: D 313 MET cc_start: 0.9063 (tpp) cc_final: 0.8672 (ttt) REVERT: D 499 MET cc_start: 0.8473 (ptm) cc_final: 0.8084 (ptm) REVERT: D 514 TYR cc_start: 0.8063 (m-10) cc_final: 0.7364 (m-80) REVERT: D 540 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8766 (mp10) REVERT: E 205 PHE cc_start: 0.7961 (t80) cc_final: 0.7541 (t80) REVERT: E 263 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: E 352 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8864 (mt) REVERT: E 422 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6532 (t80) REVERT: F 205 PHE cc_start: 0.7904 (t80) cc_final: 0.7426 (t80) REVERT: F 263 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: F 325 ILE cc_start: 0.8663 (pt) cc_final: 0.7965 (mt) REVERT: F 335 MET cc_start: 0.6338 (tmm) cc_final: 0.5728 (tpt) outliers start: 65 outliers final: 47 residues processed: 164 average time/residue: 0.1645 time to fit residues: 46.0718 Evaluate side-chains 156 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 99 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 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 235 VAL 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 538 VAL 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 538 VAL Chi-restraints excluded: chain D residue 540 GLN 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 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 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 263 GLN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 235 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 221 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 388 ASN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN ** 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 = 0.3560 r_free = 0.3560 target = 0.115201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087950 restraints weight = 54624.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.086193 restraints weight = 59997.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.087380 restraints weight = 68810.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.087921 restraints weight = 40312.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.089510 restraints weight = 35189.671| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3800 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= 0.142 Angle : 0.595 17.194 39804 Z= 0.302 Chirality : 0.043 0.419 4354 Planarity : 0.003 0.040 5106 Dihedral : 4.932 64.511 3874 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.17 % Allowed : 13.59 % Favored : 84.24 % Cbeta Deviations : 0.00 % 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: 0.84 (0.14), residues: 3560 helix: 2.05 (0.12), residues: 1694 sheet: -0.51 (0.29), residues: 344 loop : -0.93 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.068 0.001 TYR F 525 PHE 0.019 0.001 PHE D 22 TRP 0.016 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (29360) covalent geometry : angle 0.57778 / 0.30 (39664) SS BOND : bond 0.00405 / 0.22 ( 46) SS BOND : angle 1.46518 / 0.84 ( 92) hydrogen bonds : bond 0.05401 / 3.59 ( 1414) hydrogen bonds : angle 4.36558 / 3.05 ( 4194) link_BETA1-4 : bond 0.00593 / 0.31 ( 6) link_BETA1-4 : angle 3.02410 / 1.70 ( 18) link_NAG-ASN : bond 0.00858 / 0.43 ( 10) link_NAG-ASN : angle 4.03433 / 2.71 ( 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 175 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 107 time to evaluate : 1.173 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 388 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8494 (m-40) REVERT: A 432 MET cc_start: 0.8191 (mtm) cc_final: 0.7513 (ttm) REVERT: A 474 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8754 (pp) REVERT: A 671 MET cc_start: 0.9015 (mmm) cc_final: 0.8722 (mmt) REVERT: B 126 ASP cc_start: 0.7752 (t70) cc_final: 0.7475 (t0) REVERT: B 474 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8625 (pp) REVERT: B 679 MET cc_start: 0.8877 (mtt) cc_final: 0.8573 (mtm) REVERT: C 62 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8209 (pp) REVERT: C 112 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8798 (tm) REVERT: C 309 MET cc_start: 0.8625 (ttm) cc_final: 0.8363 (mtp) REVERT: C 499 MET cc_start: 0.8453 (ptm) cc_final: 0.8085 (ptm) REVERT: C 514 TYR cc_start: 0.8115 (m-10) cc_final: 0.7337 (m-80) REVERT: D 62 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8253 (pp) REVERT: D 309 MET cc_start: 0.8654 (ttm) cc_final: 0.8282 (mtp) REVERT: D 313 MET cc_start: 0.9052 (tpp) cc_final: 0.8644 (ttt) REVERT: D 354 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (tttm) REVERT: D 499 MET cc_start: 0.8456 (ptm) cc_final: 0.8060 (ptm) REVERT: D 514 TYR cc_start: 0.8098 (m-10) cc_final: 0.7348 (m-80) REVERT: E 205 PHE cc_start: 0.8084 (t80) cc_final: 0.7591 (t80) REVERT: E 263 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: E 352 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8814 (mt) REVERT: E 422 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6482 (t80) REVERT: F 205 PHE cc_start: 0.7953 (t80) cc_final: 0.7385 (t80) REVERT: F 263 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: F 325 ILE cc_start: 0.8645 (pt) cc_final: 0.7968 (mt) outliers start: 68 outliers final: 51 residues processed: 173 average time/residue: 0.1648 time to fit residues: 49.5066 Evaluate side-chains 160 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 98 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 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 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 474 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 235 VAL 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 538 VAL 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 235 VAL 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 540 GLN 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 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 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 263 GLN Chi-restraints excluded: chain F residue 461 LEU 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 206 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 302 optimal weight: 0.4980 chunk 288 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087208 restraints weight = 53279.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086108 restraints weight = 91062.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.086670 restraints weight = 80320.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087076 restraints weight = 54204.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089769 restraints weight = 48615.655| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29422 Z= 0.153 Angle : 0.594 12.357 39804 Z= 0.301 Chirality : 0.043 0.394 4354 Planarity : 0.003 0.041 5106 Dihedral : 4.897 63.964 3874 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.11 % Allowed : 13.75 % Favored : 84.14 % Cbeta Deviations : 0.00 % 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: 0.87 (0.14), residues: 3560 helix: 2.09 (0.12), residues: 1694 sheet: -0.53 (0.29), residues: 344 loop : -0.93 (0.16), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.079 0.001 TYR F 525 PHE 0.017 0.001 PHE C 22 TRP 0.018 0.001 TRP B 740 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (29360) covalent geometry : angle 0.57904 / 0.30 (39664) SS BOND : bond 0.00366 / 0.22 ( 46) SS BOND : angle 1.14361 / 0.75 ( 92) hydrogen bonds : bond 0.05370 / 3.58 ( 1414) hydrogen bonds : angle 4.35272 / 3.02 ( 4194) link_BETA1-4 : bond 0.00642 / 0.34 ( 6) link_BETA1-4 : angle 2.95665 / 1.67 ( 18) link_NAG-ASN : bond 0.00768 / 0.38 ( 10) link_NAG-ASN : angle 3.98315 / 2.70 ( 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 167 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 MET cc_start: 0.8290 (mtm) cc_final: 0.7572 (ttm) REVERT: A 474 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8683 (pp) REVERT: A 671 MET cc_start: 0.9023 (mmm) cc_final: 0.8743 (mmt) REVERT: B 126 ASP cc_start: 0.7714 (t70) cc_final: 0.7450 (t0) REVERT: B 474 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8636 (pp) REVERT: B 679 MET cc_start: 0.8794 (mtt) cc_final: 0.8482 (mtm) REVERT: C 62 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8269 (pp) REVERT: C 112 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8737 (tm) REVERT: C 309 MET cc_start: 0.8659 (ttm) cc_final: 0.8348 (mtp) REVERT: C 499 MET cc_start: 0.8442 (ptm) cc_final: 0.8085 (ptm) REVERT: C 514 TYR cc_start: 0.8051 (m-10) cc_final: 0.7325 (m-80) REVERT: D 62 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8271 (pp) REVERT: D 309 MET cc_start: 0.8666 (ttm) cc_final: 0.8276 (mtp) REVERT: D 313 MET cc_start: 0.9053 (tpp) cc_final: 0.8672 (ttt) REVERT: D 354 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8403 (tttm) REVERT: D 499 MET cc_start: 0.8433 (ptm) cc_final: 0.8057 (ptm) REVERT: D 514 TYR cc_start: 0.8016 (m-10) cc_final: 0.7307 (m-80) REVERT: E 205 PHE cc_start: 0.7630 (t80) cc_final: 0.7284 (t80) REVERT: E 263 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: E 352 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8876 (mt) REVERT: E 422 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6341 (t80) REVERT: F 205 PHE cc_start: 0.7497 (t80) cc_final: 0.7111 (t80) REVERT: F 263 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: F 325 ILE cc_start: 0.8521 (pt) cc_final: 0.7864 (mt) REVERT: F 335 MET cc_start: 0.6690 (tpt) cc_final: 0.6488 (tpp) outliers start: 66 outliers final: 53 residues processed: 163 average time/residue: 0.1670 time to fit residues: 46.8131 Evaluate side-chains 161 residues out of total 3128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 98 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 474 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 235 VAL 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 538 VAL 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 235 VAL 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 540 GLN 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 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 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 263 GLN Chi-restraints excluded: chain F residue 461 LEU 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: 2.9990 chunk 38 optimal weight: 0.6980 chunk 310 optimal weight: 0.6980 chunk 339 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 353 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 347 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 ASN E 566 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086156 restraints weight = 53623.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.084931 restraints weight = 75328.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.085615 restraints weight = 87716.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086098 restraints weight = 54122.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.088396 restraints weight = 44909.823| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29422 Z= 0.148 Angle : 0.613 18.681 39804 Z= 0.311 Chirality : 0.043 0.369 4354 Planarity : 0.003 0.041 5106 Dihedral : 4.876 62.678 3874 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 13.78 % Favored : 84.14 % Cbeta Deviations : 0.03 % 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: 0.89 (0.14), residues: 3560 helix: 2.08 (0.12), residues: 1698 sheet: -0.52 (0.29), residues: 344 loop : -0.89 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 623 TYR 0.072 0.001 TYR F 525 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/Z covalent geometry : bond 0.00331 / 0.15 (29360) covalent geometry : angle 0.59667 / 0.31 (39664) SS BOND : bond 0.00465 / 0.29 ( 46) SS BOND : angle 1.63026 / 1.05 ( 92) hydrogen bonds : bond 0.05425 / 3.61 ( 1414) hydrogen bonds : angle 4.36194 / 3.05 ( 4194) link_BETA1-4 : bond 0.00686 / 0.36 ( 6) link_BETA1-4 : angle 2.83802 / 1.60 ( 18) link_NAG-ASN : bond 0.00774 / 0.39 ( 10) link_NAG-ASN : angle 3.86997 / 2.64 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3627.63 seconds wall clock time: 64 minutes 17.71 seconds (3857.71 seconds total)