Starting phenix.real_space_refine on Sat Feb 7 17:01:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xz9_38790/02_2026/8xz9_38790.map" } resolution = 3.37 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= -0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 174 5.16 5 C 22421 2.51 5 N 5792 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35083 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4906 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 24, 'TRANS': 571} Chain: "B" Number of atoms: 8320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8320 Classifications: {'peptide': 1063} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 8316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1063, 8316 Classifications: {'peptide': 1063} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 55, 'TRANS': 1007} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4897 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 24, 'TRANS': 570} Chain breaks: 1 Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.59, per 1000 atoms: 0.22 Number of scatterers: 35083 At special positions: 0 Unit cell: (154, 164, 233, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 174 16.00 O 6696 8.00 N 5792 7.00 C 22421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.02 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D 840 " - pdb=" SG CYS D 851 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 343 " - pdb=" SG CYS E 360 " 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 F 1 " - " BMA F 2 " " NAG G 1 " - " BMA G 2 " " NAG H 1 " - " BMA H 2 " " NAG I 1 " - " BMA I 2 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " BMA M 2 " " NAG N 1 " - " BMA N 2 " " NAG O 1 " - " BMA O 2 " " NAG P 1 " - " BMA P 2 " " NAG Q 1 " - " BMA Q 2 " " NAG R 1 " - " BMA R 2 " NAG-ASN " NAG F 1 " - " ASN C1134 " " NAG G 1 " - " ASN C1098 " " NAG H 1 " - " ASN D1134 " " NAG I 1 " - " ASN D 801 " " NAG J 1 " - " ASN D1098 " " NAG K 1 " - " ASN D 717 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN D 354 " " NAG R 1 " - " ASN D 282 " Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8222 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 50 sheets defined 35.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.622A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.590A pdb=" N SER A 106 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 156 through 193 removed outlier: 3.979A pdb=" N LYS A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.506A pdb=" N GLU A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 217 through 251 removed outlier: 4.224A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Proline residue: A 234 - end of helix removed outlier: 3.527A pdb=" N THR A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 292 through 300 Processing helix chain 'A' and resid 302 through 317 Processing helix chain 'A' and resid 323 through 330 removed outlier: 3.714A pdb=" N TRP A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 384 removed outlier: 3.967A pdb=" N PHE A 368 " --> pdb=" O THR A 364 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 384 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 413 Processing helix chain 'A' and resid 413 through 421 removed outlier: 3.604A pdb=" N LEU A 417 " --> pdb=" O THR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 447 removed outlier: 4.436A pdb=" N ILE A 445 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 465 removed outlier: 4.361A pdb=" N PHE A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP A 458 " --> pdb=" O MET A 454 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A 465 " --> pdb=" O MET A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.830A pdb=" N CYS A 501 " --> pdb=" O ASP A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.524A pdb=" N PHE A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 4.066A pdb=" N MET A 556 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 removed outlier: 3.645A pdb=" N SER A 562 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 563 " --> pdb=" O GLY A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 563' Processing helix chain 'A' and resid 564 through 573 removed outlier: 4.318A pdb=" N ALA A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 removed outlier: 4.107A pdb=" N LEU A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 598 removed outlier: 3.909A pdb=" N GLU A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 597 " --> pdb=" O TRP A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.580A pdb=" N VAL B 407 " --> pdb=" O LYS B 403 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 627 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.606A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.539A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.627A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.615A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1139 through 1144 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.587A pdb=" N SER C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 546 Processing helix chain 'C' and resid 616 through 627 removed outlier: 3.737A pdb=" N VAL C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.764A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 760 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.964A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.521A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1139 through 1144 removed outlier: 3.740A pdb=" N LEU C1143 " --> pdb=" O ASP C1139 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1139 through 1144' Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 365 through 372 removed outlier: 3.784A pdb=" N TYR D 369 " --> pdb=" O SER D 366 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN D 370 " --> pdb=" O VAL D 367 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 372 " --> pdb=" O TYR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 616 through 627 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.754A pdb=" N TYR D 741 " --> pdb=" O ASP D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 754 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 759 through 783 removed outlier: 4.095A pdb=" N LEU D 763 " --> pdb=" O PHE D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 825 Processing helix chain 'D' and resid 848 through 854 removed outlier: 3.738A pdb=" N ALA D 852 " --> pdb=" O ASP D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 890 Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 919 removed outlier: 3.821A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 941 Processing helix chain 'D' and resid 945 through 965 Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1033 removed outlier: 5.326A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN D 992 " --> pdb=" O GLU D 988 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 52 removed outlier: 3.832A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.615A pdb=" N SER E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 193 Proline residue: E 177 - end of helix Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'E' and resid 218 through 251 removed outlier: 4.025A pdb=" N MET E 222 " --> pdb=" O ARG E 218 " (cutoff:3.500A) Proline residue: E 234 - end of helix Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.678A pdb=" N VAL E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 300 Processing helix chain 'E' and resid 302 through 316 Processing helix chain 'E' and resid 323 through 330 removed outlier: 3.860A pdb=" N TRP E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 373 removed outlier: 3.720A pdb=" N PHE E 368 " --> pdb=" O THR E 364 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU E 369 " --> pdb=" O MET E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 3.915A pdb=" N TYR E 384 " --> pdb=" O TYR E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 413 removed outlier: 4.361A pdb=" N MET E 407 " --> pdb=" O VAL E 403 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 408 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR E 413 " --> pdb=" O LEU E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 420 removed outlier: 3.917A pdb=" N LEU E 417 " --> pdb=" O THR E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 446 Processing helix chain 'E' and resid 447 through 465 removed outlier: 4.254A pdb=" N PHE E 451 " --> pdb=" O GLY E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 483 Processing helix chain 'E' and resid 497 through 501 removed outlier: 3.970A pdb=" N CYS E 501 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 Processing helix chain 'E' and resid 512 through 533 Processing helix chain 'E' and resid 546 through 560 removed outlier: 4.308A pdb=" N LEU E 559 " --> pdb=" O GLN E 555 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY E 560 " --> pdb=" O MET E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 571 Processing helix chain 'E' and resid 580 through 587 removed outlier: 4.066A pdb=" N PHE E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 587 through 597 Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 removed outlier: 3.693A pdb=" N VAL A 132 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 261 through 262 removed outlier: 6.771A pdb=" N LEU A 261 " --> pdb=" O VAL A 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 349 through 351 removed outlier: 6.136A pdb=" N ASP A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 3.605A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.915A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 316 removed outlier: 7.256A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.346A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 396 through 402 removed outlier: 3.574A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 430 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.020A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.563A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 713 through 715 removed outlier: 3.958A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.366A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.151A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1077 through 1078 removed outlier: 4.386A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.559A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N THR C 95 " --> pdb=" O ASP C 264 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.655A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.128A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.261A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.704A pdb=" N ALA C 397 " --> pdb=" O THR C 356 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 435 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 703 through 704 removed outlier: 7.283A pdb=" N ASN C 703 " --> pdb=" O LYS D 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 713 through 715 removed outlier: 3.857A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.868A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.002A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'D' and resid 28 through 30 removed outlier: 7.714A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 65 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N THR D 95 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 227 " --> pdb=" O ILE D 203 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.506A pdb=" N ASP D 53 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.906A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 130 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE D 168 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 311 through 316 removed outlier: 6.899A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 324 through 325 removed outlier: 7.451A pdb=" N GLU D 324 " --> pdb=" O ASN D 540 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N ASN D 542 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 543 " --> pdb=" O LEU D 546 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.535A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 397 " --> pdb=" O THR D 356 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP D 436 " --> pdb=" O ARG D 509 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 452 through 454 removed outlier: 4.194A pdb=" N TYR D 453 " --> pdb=" O GLN D 493 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 493 " --> pdb=" O TYR D 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'D' and resid 654 through 655 Processing sheet with id=AE8, first strand: chain 'D' and resid 713 through 715 removed outlier: 3.637A pdb=" N ILE D 714 " --> pdb=" O LYS D1073 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D1073 " --> pdb=" O ILE D 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 718 through 728 removed outlier: 7.334A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 733 through 734 removed outlier: 4.267A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AF4, first strand: chain 'E' and resid 131 through 133 removed outlier: 3.991A pdb=" N VAL E 132 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU E 141 " --> pdb=" O VAL E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'E' and resid 261 through 262 removed outlier: 6.179A pdb=" N LEU E 261 " --> pdb=" O VAL E 487 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1393 hydrogen bonds defined for protein. 3975 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: 9.88 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11184 1.34 - 1.47: 9231 1.47 - 1.60: 15296 1.60 - 1.73: 0 1.73 - 1.86: 245 Bond restraints: 35956 Sorted by residual: bond pdb=" N TYR C 489 " pdb=" CA TYR C 489 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.25e-02 6.40e+03 6.72e+00 bond pdb=" N TYR B 489 " pdb=" CA TYR B 489 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.18e-02 7.18e+03 6.60e+00 bond pdb=" N THR A 27 " pdb=" CA THR A 27 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.68e+00 bond pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.19e-02 7.06e+03 5.10e+00 bond pdb=" N LYS A 26 " pdb=" CA LYS A 26 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.05e+00 ... (remaining 35951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 48190 2.28 - 4.55: 581 4.55 - 6.83: 97 6.83 - 9.10: 14 9.10 - 11.38: 4 Bond angle restraints: 48886 Sorted by residual: angle pdb=" CA PRO C 209 " pdb=" N PRO C 209 " pdb=" CD PRO C 209 " ideal model delta sigma weight residual 112.00 103.99 8.01 1.40e+00 5.10e-01 3.28e+01 angle pdb=" C GLU B 471 " pdb=" CA GLU B 471 " pdb=" CB GLU B 471 " ideal model delta sigma weight residual 117.23 110.39 6.84 1.36e+00 5.41e-01 2.53e+01 angle pdb=" N ILE A 317 " pdb=" CA ILE A 317 " pdb=" C ILE A 317 " ideal model delta sigma weight residual 111.91 108.39 3.52 8.90e-01 1.26e+00 1.56e+01 angle pdb=" CB MET A 473 " pdb=" CG MET A 473 " pdb=" SD MET A 473 " ideal model delta sigma weight residual 112.70 124.08 -11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" CA GLU B 471 " pdb=" C GLU B 471 " pdb=" N ILE B 472 " ideal model delta sigma weight residual 119.98 116.77 3.21 8.50e-01 1.38e+00 1.42e+01 ... (remaining 48881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.23: 18949 22.23 - 44.45: 2256 44.45 - 66.68: 289 66.68 - 88.91: 138 88.91 - 111.14: 59 Dihedral angle restraints: 21691 sinusoidal: 8899 harmonic: 12792 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 12.62 80.38 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS D 662 " pdb=" SG CYS D 662 " pdb=" SG CYS D 671 " pdb=" CB CYS D 671 " ideal model delta sinusoidal sigma weight residual -86.00 -14.49 -71.51 1 1.00e+01 1.00e-02 6.56e+01 dihedral pdb=" CB CYS D 480 " pdb=" SG CYS D 480 " pdb=" SG CYS D 488 " pdb=" CB CYS D 488 " ideal model delta sinusoidal sigma weight residual 93.00 21.74 71.26 1 1.00e+01 1.00e-02 6.52e+01 ... (remaining 21688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 5448 0.152 - 0.303: 24 0.303 - 0.455: 0 0.455 - 0.606: 0 0.606 - 0.758: 3 Chirality restraints: 5475 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN D1098 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.99e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.42e+00 ... (remaining 5472 not shown) Planarity restraints: 6285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 208 " 0.096 5.00e-02 4.00e+02 1.40e-01 3.14e+01 pdb=" N PRO C 209 " -0.242 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 388 " 0.012 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C PRO A 388 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 388 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR A 389 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 487 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.81e+00 pdb=" C ASN C 487 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN C 487 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS C 488 " 0.014 2.00e-02 2.50e+03 ... (remaining 6282 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1028 2.70 - 3.25: 35266 3.25 - 3.80: 58106 3.80 - 4.35: 72544 4.35 - 4.90: 120864 Nonbonded interactions: 287808 Sorted by model distance: nonbonded pdb=" OG SER A 217 " pdb=" OD1 ASP A 219 " model vdw 2.146 3.040 nonbonded pdb=" O PHE B 377 " pdb=" OH TYR D 489 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR D 323 " pdb=" OE1 GLU D 324 " model vdw 2.156 3.040 nonbonded pdb=" NE2 GLN C 474 " pdb=" O LYS C 478 " model vdw 2.174 3.120 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.179 3.040 ... (remaining 287803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 373 or resid 375 through 614)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 23 through 99 or (resid 100 and (name N or name CA or name \ C or name O )) or resid 101 through 1144)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) } 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 individual isotropic 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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 34.250 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.003 0.102 36022 Z= 0.143 Angle : 0.624 12.205 49044 Z= 0.310 Chirality : 0.047 0.758 5475 Planarity : 0.004 0.140 6272 Dihedral : 19.784 111.136 13349 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 0.37 % Allowed : 29.83 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4344 helix: 1.44 (0.14), residues: 1445 sheet: -0.54 (0.22), residues: 586 loop : -1.57 (0.13), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 392 TYR 0.023 0.001 TYR B 489 PHE 0.040 0.001 PHE E 307 TRP 0.020 0.001 TRP A 476 HIS 0.003 0.000 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00295 (35956) covalent geometry : angle 0.60753 (48886) SS BOND : bond 0.00413 ( 40) SS BOND : angle 1.51174 ( 80) hydrogen bonds : bond 0.14537 ( 1383) hydrogen bonds : angle 6.35949 ( 3975) link_BETA1-4 : bond 0.00358 ( 13) link_BETA1-4 : angle 2.32104 ( 39) link_NAG-ASN : bond 0.00580 ( 13) link_NAG-ASN : angle 4.06449 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 856 ASN cc_start: 0.8414 (m110) cc_final: 0.8213 (m110) REVERT: E 151 MET cc_start: 0.1047 (tmm) cc_final: 0.0690 (tmm) REVERT: E 274 TRP cc_start: 0.0047 (OUTLIER) cc_final: -0.0613 (m100) outliers start: 14 outliers final: 4 residues processed: 235 average time/residue: 0.1832 time to fit residues: 73.9994 Evaluate side-chains 208 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 203 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain E residue 274 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN B 314 GLN B 901 GLN B1054 GLN B1074 ASN C 165 ASN D 343 ASN D 804 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.183521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.132987 restraints weight = 81503.797| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 3.41 r_work: 0.3492 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36022 Z= 0.143 Angle : 0.598 13.220 49044 Z= 0.296 Chirality : 0.045 0.552 5475 Planarity : 0.004 0.092 6272 Dihedral : 10.186 83.469 5254 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 3.35 % Allowed : 26.69 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.13), residues: 4344 helix: 1.41 (0.14), residues: 1448 sheet: -0.56 (0.22), residues: 585 loop : -1.52 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 634 TYR 0.022 0.001 TYR B1067 PHE 0.035 0.001 PHE E 524 TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00322 (35956) covalent geometry : angle 0.57607 (48886) SS BOND : bond 0.00389 ( 40) SS BOND : angle 1.59964 ( 80) hydrogen bonds : bond 0.03893 ( 1383) hydrogen bonds : angle 5.18583 ( 3975) link_BETA1-4 : bond 0.00554 ( 13) link_BETA1-4 : angle 3.34079 ( 39) link_NAG-ASN : bond 0.00352 ( 13) link_NAG-ASN : angle 4.24420 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 226 time to evaluate : 1.247 Fit side-chains REVERT: B 91 TYR cc_start: 0.8377 (OUTLIER) cc_final: 0.7778 (t80) REVERT: B 878 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8083 (mt) REVERT: C 849 LEU cc_start: 0.2276 (OUTLIER) cc_final: 0.1927 (pp) REVERT: C 1017 GLU cc_start: 0.8562 (tt0) cc_final: 0.8349 (tm-30) REVERT: C 1073 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8409 (ptmm) REVERT: D 104 TRP cc_start: 0.8301 (m-90) cc_final: 0.8033 (m-90) REVERT: E 222 MET cc_start: 0.0121 (mpp) cc_final: -0.1225 (tmm) REVERT: E 329 ASN cc_start: 0.2796 (m-40) cc_final: 0.2508 (p0) REVERT: E 391 LEU cc_start: 0.3274 (mt) cc_final: 0.3042 (mm) REVERT: E 467 ILE cc_start: 0.2514 (OUTLIER) cc_final: 0.1921 (tt) REVERT: E 556 MET cc_start: 0.2358 (tpt) cc_final: 0.1451 (mmm) outliers start: 128 outliers final: 45 residues processed: 337 average time/residue: 0.1857 time to fit residues: 107.9495 Evaluate side-chains 259 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 515 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 221 optimal weight: 20.0000 chunk 145 optimal weight: 0.9990 chunk 305 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 86 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 264 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN ** D1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** 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 = 0.4497 r_free = 0.4497 target = 0.172965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.122076 restraints weight = 79997.315| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.06 r_work: 0.3501 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36022 Z= 0.110 Angle : 0.573 12.924 49044 Z= 0.281 Chirality : 0.045 0.554 5475 Planarity : 0.004 0.046 6272 Dihedral : 7.469 74.391 5251 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.82 % Favored : 94.08 % Rotamer: Outliers : 3.06 % Allowed : 27.14 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.13), residues: 4344 helix: 1.48 (0.14), residues: 1446 sheet: -0.59 (0.22), residues: 578 loop : -1.51 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 847 TYR 0.020 0.001 TYR E 384 PHE 0.029 0.001 PHE B 464 TRP 0.016 0.001 TRP A 476 HIS 0.003 0.000 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00241 (35956) covalent geometry : angle 0.55155 (48886) SS BOND : bond 0.00356 ( 40) SS BOND : angle 1.42517 ( 80) hydrogen bonds : bond 0.03620 ( 1383) hydrogen bonds : angle 4.91097 ( 3975) link_BETA1-4 : bond 0.00460 ( 13) link_BETA1-4 : angle 3.36422 ( 39) link_NAG-ASN : bond 0.00372 ( 13) link_NAG-ASN : angle 4.08181 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 230 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.0238 (m-10) cc_final: -0.0250 (m-10) REVERT: C 265 TYR cc_start: 0.5702 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: C 856 ASN cc_start: 0.8324 (m110) cc_final: 0.8103 (m110) REVERT: C 869 MET cc_start: 0.9183 (mtp) cc_final: 0.8970 (mtm) REVERT: C 878 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8723 (tt) REVERT: D 580 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: D 850 ILE cc_start: -0.0115 (OUTLIER) cc_final: -0.0405 (mm) REVERT: E 222 MET cc_start: 0.0109 (mpp) cc_final: -0.1228 (tmm) REVERT: E 269 MET cc_start: 0.0717 (mtt) cc_final: -0.0345 (ttm) REVERT: E 284 PHE cc_start: 0.0440 (OUTLIER) cc_final: 0.0215 (t80) REVERT: E 329 ASN cc_start: 0.2772 (m-40) cc_final: 0.2473 (p0) REVERT: E 467 ILE cc_start: 0.2600 (OUTLIER) cc_final: 0.1999 (tt) REVERT: E 556 MET cc_start: 0.2314 (tpt) cc_final: 0.1477 (mmm) outliers start: 117 outliers final: 57 residues processed: 329 average time/residue: 0.1873 time to fit residues: 106.7641 Evaluate side-chains 269 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 206 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 515 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 235 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 305 optimal weight: 7.9990 chunk 218 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN B1074 ASN C 321 GLN C1005 GLN C1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1036 GLN D1074 ASN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.172494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123624 restraints weight = 79584.470| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.71 r_work: 0.3441 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36022 Z= 0.128 Angle : 0.567 13.115 49044 Z= 0.280 Chirality : 0.044 0.566 5475 Planarity : 0.004 0.048 6272 Dihedral : 5.666 61.167 5251 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.89 % Favored : 94.01 % Rotamer: Outliers : 4.05 % Allowed : 26.75 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4344 helix: 1.48 (0.14), residues: 1444 sheet: -0.63 (0.22), residues: 586 loop : -1.50 (0.13), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE B 464 TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00289 (35956) covalent geometry : angle 0.54419 (48886) SS BOND : bond 0.00368 ( 40) SS BOND : angle 1.56160 ( 80) hydrogen bonds : bond 0.03554 ( 1383) hydrogen bonds : angle 4.80039 ( 3975) link_BETA1-4 : bond 0.00421 ( 13) link_BETA1-4 : angle 3.25840 ( 39) link_NAG-ASN : bond 0.00456 ( 13) link_NAG-ASN : angle 4.19405 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 220 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 463 PHE cc_start: 0.0230 (m-10) cc_final: -0.0212 (m-10) REVERT: B 91 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7790 (t80) REVERT: B 513 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7228 (pp) REVERT: C 265 TYR cc_start: 0.5782 (OUTLIER) cc_final: 0.4992 (m-80) REVERT: C 489 TYR cc_start: 0.2591 (OUTLIER) cc_final: 0.1971 (m-80) REVERT: C 849 LEU cc_start: 0.2012 (OUTLIER) cc_final: 0.1640 (pp) REVERT: C 856 ASN cc_start: 0.8414 (m110) cc_final: 0.8197 (m110) REVERT: C 869 MET cc_start: 0.9188 (mtp) cc_final: 0.8981 (mtm) REVERT: D 580 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: D 850 ILE cc_start: -0.0153 (OUTLIER) cc_final: -0.0428 (mm) REVERT: D 1005 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8317 (mp10) REVERT: E 69 TRP cc_start: 0.3973 (OUTLIER) cc_final: 0.3577 (t60) REVERT: E 222 MET cc_start: 0.0154 (mpp) cc_final: -0.1194 (tmm) REVERT: E 269 MET cc_start: 0.0668 (mtt) cc_final: -0.0419 (ttm) REVERT: E 284 PHE cc_start: 0.0575 (OUTLIER) cc_final: 0.0335 (t80) REVERT: E 329 ASN cc_start: 0.2742 (m-40) cc_final: 0.2451 (p0) REVERT: E 467 ILE cc_start: 0.2483 (OUTLIER) cc_final: 0.1825 (tt) REVERT: E 556 MET cc_start: 0.2577 (tpt) cc_final: 0.2276 (ppp) outliers start: 155 outliers final: 92 residues processed: 353 average time/residue: 0.1938 time to fit residues: 118.5553 Evaluate side-chains 307 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 204 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 274 TRP Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 423 optimal weight: 9.9990 chunk 345 optimal weight: 0.7980 chunk 402 optimal weight: 0.3980 chunk 259 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 145 optimal weight: 0.0970 chunk 397 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 256 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 556 ASN C1005 GLN C1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN D1005 GLN D1036 GLN E 89 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.181625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.131570 restraints weight = 76714.022| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.83 r_work: 0.3484 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 36022 Z= 0.122 Angle : 0.558 13.118 49044 Z= 0.277 Chirality : 0.044 0.569 5475 Planarity : 0.004 0.049 6272 Dihedral : 5.008 48.750 5251 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 4.10 % Allowed : 27.11 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4344 helix: 1.55 (0.14), residues: 1438 sheet: -0.65 (0.22), residues: 586 loop : -1.47 (0.13), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 319 TYR 0.017 0.001 TYR D 380 PHE 0.023 0.001 PHE B 464 TRP 0.015 0.001 TRP A 476 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00274 (35956) covalent geometry : angle 0.53735 (48886) SS BOND : bond 0.00517 ( 40) SS BOND : angle 1.51878 ( 80) hydrogen bonds : bond 0.03487 ( 1383) hydrogen bonds : angle 4.70864 ( 3975) link_BETA1-4 : bond 0.00461 ( 13) link_BETA1-4 : angle 2.87771 ( 39) link_NAG-ASN : bond 0.00391 ( 13) link_NAG-ASN : angle 4.12549 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 218 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: 0.0118 (m-10) cc_final: -0.0289 (m-10) REVERT: B 91 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7677 (t80) REVERT: C 265 TYR cc_start: 0.5804 (OUTLIER) cc_final: 0.4998 (m-80) REVERT: C 489 TYR cc_start: 0.2631 (OUTLIER) cc_final: 0.2047 (m-80) REVERT: C 856 ASN cc_start: 0.8414 (m110) cc_final: 0.8205 (m110) REVERT: D 346 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7184 (tpm170) REVERT: D 580 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: D 850 ILE cc_start: -0.0237 (OUTLIER) cc_final: -0.0521 (mm) REVERT: E 69 TRP cc_start: 0.3888 (OUTLIER) cc_final: 0.3571 (t60) REVERT: E 222 MET cc_start: 0.0433 (mpp) cc_final: -0.0962 (tmm) REVERT: E 269 MET cc_start: 0.0876 (mtt) cc_final: -0.0214 (ttm) REVERT: E 284 PHE cc_start: 0.0722 (OUTLIER) cc_final: 0.0424 (t80) REVERT: E 467 ILE cc_start: 0.2443 (OUTLIER) cc_final: 0.1887 (tt) REVERT: E 556 MET cc_start: 0.2720 (tpt) cc_final: 0.2493 (ppp) outliers start: 157 outliers final: 108 residues processed: 354 average time/residue: 0.1921 time to fit residues: 118.0652 Evaluate side-chains 316 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 199 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 170 TYR Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1005 GLN Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 154 optimal weight: 0.7980 chunk 292 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 379 optimal weight: 20.0000 chunk 261 optimal weight: 1.9990 chunk 424 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 298 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1074 ASN D 125 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1036 GLN E 89 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.173569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122556 restraints weight = 80319.571| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.54 r_work: 0.3456 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36022 Z= 0.161 Angle : 0.585 13.496 49044 Z= 0.290 Chirality : 0.044 0.589 5475 Planarity : 0.004 0.053 6272 Dihedral : 4.788 46.902 5249 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.83 % Rotamer: Outliers : 4.05 % Allowed : 27.58 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4344 helix: 1.53 (0.14), residues: 1436 sheet: -0.69 (0.21), residues: 592 loop : -1.52 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 102 TYR 0.021 0.001 TYR E 384 PHE 0.021 0.001 PHE B 464 TRP 0.016 0.001 TRP E 274 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00368 (35956) covalent geometry : angle 0.56391 (48886) SS BOND : bond 0.00394 ( 40) SS BOND : angle 1.64565 ( 80) hydrogen bonds : bond 0.03601 ( 1383) hydrogen bonds : angle 4.73641 ( 3975) link_BETA1-4 : bond 0.00413 ( 13) link_BETA1-4 : angle 2.65116 ( 39) link_NAG-ASN : bond 0.00421 ( 13) link_NAG-ASN : angle 4.29842 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 204 time to evaluate : 1.329 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 79 MET cc_start: 0.1315 (OUTLIER) cc_final: 0.0964 (mtm) REVERT: A 463 PHE cc_start: 0.0235 (m-10) cc_final: -0.0183 (m-10) REVERT: B 28 TYR cc_start: 0.7755 (OUTLIER) cc_final: 0.7470 (t80) REVERT: B 654 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8315 (pt0) REVERT: B 1142 GLN cc_start: 0.8752 (mm110) cc_final: 0.8451 (mm-40) REVERT: C 102 ARG cc_start: 0.5326 (ptt180) cc_final: 0.4474 (mpp80) REVERT: C 489 TYR cc_start: 0.2487 (OUTLIER) cc_final: 0.1862 (m-80) REVERT: C 557 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8759 (mttm) REVERT: D 580 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: D 850 ILE cc_start: -0.0178 (OUTLIER) cc_final: -0.0454 (mm) REVERT: D 1002 GLN cc_start: 0.8659 (tp40) cc_final: 0.8307 (tm-30) REVERT: E 69 TRP cc_start: 0.4055 (OUTLIER) cc_final: 0.3629 (t60) REVERT: E 284 PHE cc_start: 0.0501 (OUTLIER) cc_final: 0.0233 (t80) REVERT: E 467 ILE cc_start: 0.2444 (OUTLIER) cc_final: 0.1850 (tt) REVERT: E 556 MET cc_start: 0.2639 (tpt) cc_final: 0.2411 (ppp) outliers start: 155 outliers final: 110 residues processed: 342 average time/residue: 0.1961 time to fit residues: 116.0016 Evaluate side-chains 313 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 193 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1134 ASN Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 327 TRP Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 522 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 242 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 61 optimal weight: 0.0030 chunk 372 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 391 optimal weight: 20.0000 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.174643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.123804 restraints weight = 77687.479| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 3.30 r_work: 0.3495 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36022 Z= 0.141 Angle : 0.574 13.478 49044 Z= 0.285 Chirality : 0.044 0.599 5475 Planarity : 0.004 0.054 6272 Dihedral : 4.653 44.816 5249 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.92 % Favored : 93.97 % Rotamer: Outliers : 4.26 % Allowed : 27.29 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.13), residues: 4344 helix: 1.54 (0.14), residues: 1430 sheet: -0.73 (0.21), residues: 593 loop : -1.50 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 319 TYR 0.017 0.001 TYR E 384 PHE 0.022 0.001 PHE B 464 TRP 0.016 0.001 TRP A 476 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00323 (35956) covalent geometry : angle 0.55445 (48886) SS BOND : bond 0.00407 ( 40) SS BOND : angle 1.57499 ( 80) hydrogen bonds : bond 0.03539 ( 1383) hydrogen bonds : angle 4.70861 ( 3975) link_BETA1-4 : bond 0.00506 ( 13) link_BETA1-4 : angle 2.45495 ( 39) link_NAG-ASN : bond 0.00369 ( 13) link_NAG-ASN : angle 4.23257 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 204 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: -0.0042 (m-10) cc_final: -0.0419 (m-10) REVERT: B 28 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7447 (t80) REVERT: B 389 ASP cc_start: 0.6846 (OUTLIER) cc_final: 0.6278 (m-30) REVERT: B 654 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8423 (pt0) REVERT: B 740 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8008 (mtp) REVERT: B 1142 GLN cc_start: 0.8732 (mm110) cc_final: 0.8426 (mm-40) REVERT: C 102 ARG cc_start: 0.5378 (ptt180) cc_final: 0.4510 (mpp80) REVERT: C 489 TYR cc_start: 0.2827 (OUTLIER) cc_final: 0.2196 (m-80) REVERT: C 557 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8778 (mttm) REVERT: D 580 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: D 850 ILE cc_start: -0.0238 (OUTLIER) cc_final: -0.0513 (mm) REVERT: D 981 LEU cc_start: 0.8453 (mt) cc_final: 0.8144 (mt) REVERT: E 69 TRP cc_start: 0.3983 (OUTLIER) cc_final: 0.3558 (t60) REVERT: E 284 PHE cc_start: 0.0342 (OUTLIER) cc_final: 0.0095 (t80) REVERT: E 467 ILE cc_start: 0.2383 (OUTLIER) cc_final: 0.1936 (tt) REVERT: E 556 MET cc_start: 0.2650 (tpt) cc_final: 0.2363 (ppp) outliers start: 163 outliers final: 114 residues processed: 352 average time/residue: 0.1862 time to fit residues: 114.0864 Evaluate side-chains 319 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 194 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1075 PHE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 957 GLN Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1075 PHE Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 327 TRP Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 467 ILE Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 522 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 355 optimal weight: 0.8980 chunk 252 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 338 optimal weight: 3.9990 chunk 397 optimal weight: 6.9990 chunk 399 optimal weight: 5.9990 chunk 391 optimal weight: 4.9990 chunk 282 optimal weight: 5.9990 chunk 200 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 523 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 804 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 ASN C1005 GLN C1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D 978 ASN E 51 ASN E 89 GLN E 90 ASN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.166466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116211 restraints weight = 80173.157| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.50 r_work: 0.3364 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 36022 Z= 0.295 Angle : 0.713 15.336 49044 Z= 0.357 Chirality : 0.048 0.691 5475 Planarity : 0.005 0.055 6272 Dihedral : 5.194 42.309 5249 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.14 % Favored : 92.75 % Rotamer: Outliers : 4.24 % Allowed : 27.45 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4344 helix: 1.13 (0.13), residues: 1445 sheet: -1.04 (0.21), residues: 606 loop : -1.60 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 815 TYR 0.029 0.002 TYR C 265 PHE 0.021 0.002 PHE D 898 TRP 0.021 0.002 TRP B 64 HIS 0.006 0.001 HIS E 428 Details of bonding type rmsd covalent geometry : bond 0.00682 (35956) covalent geometry : angle 0.69003 (48886) SS BOND : bond 0.00509 ( 40) SS BOND : angle 2.36102 ( 80) hydrogen bonds : bond 0.04235 ( 1383) hydrogen bonds : angle 5.07544 ( 3975) link_BETA1-4 : bond 0.00405 ( 13) link_BETA1-4 : angle 2.52274 ( 39) link_NAG-ASN : bond 0.00685 ( 13) link_NAG-ASN : angle 5.02308 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 198 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: -0.0221 (m-10) cc_final: -0.0703 (m-80) REVERT: B 654 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: B 740 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8132 (mtp) REVERT: B 1142 GLN cc_start: 0.8721 (mm110) cc_final: 0.8437 (mm-40) REVERT: C 489 TYR cc_start: 0.2758 (OUTLIER) cc_final: 0.1970 (m-80) REVERT: C 557 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8600 (mttm) REVERT: C 731 MET cc_start: 0.9208 (ptt) cc_final: 0.8865 (ptt) REVERT: C 1050 MET cc_start: 0.8896 (ptt) cc_final: 0.8621 (ptm) REVERT: D 580 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7480 (mp10) REVERT: D 850 ILE cc_start: -0.0222 (OUTLIER) cc_final: -0.0539 (mm) REVERT: D 981 LEU cc_start: 0.8473 (mt) cc_final: 0.8138 (mt) REVERT: E 191 ARG cc_start: 0.2920 (tpt170) cc_final: 0.2551 (mtp180) REVERT: E 284 PHE cc_start: 0.0496 (OUTLIER) cc_final: 0.0182 (t80) REVERT: E 556 MET cc_start: 0.2653 (tpt) cc_final: 0.2297 (ppp) outliers start: 162 outliers final: 116 residues processed: 340 average time/residue: 0.1871 time to fit residues: 109.7704 Evaluate side-chains 311 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 188 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 557 LYS Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 592 PHE Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 327 TRP Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 522 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 57 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 404 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 chunk 296 optimal weight: 0.8980 chunk 328 optimal weight: 2.9990 chunk 409 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 367 optimal weight: 0.8980 chunk 366 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN D 81 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN E 89 GLN ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.169513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119379 restraints weight = 79146.958| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.42 r_work: 0.3419 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36022 Z= 0.147 Angle : 0.616 14.045 49044 Z= 0.306 Chirality : 0.046 0.662 5475 Planarity : 0.004 0.057 6272 Dihedral : 4.927 40.333 5249 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.05 % Favored : 93.83 % Rotamer: Outliers : 3.37 % Allowed : 28.47 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.13), residues: 4344 helix: 1.26 (0.14), residues: 1442 sheet: -0.97 (0.21), residues: 609 loop : -1.54 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1039 TYR 0.020 0.001 TYR C 265 PHE 0.022 0.001 PHE B 464 TRP 0.016 0.001 TRP A 476 HIS 0.005 0.001 HIS A 240 Details of bonding type rmsd covalent geometry : bond 0.00337 (35956) covalent geometry : angle 0.59554 (48886) SS BOND : bond 0.00441 ( 40) SS BOND : angle 1.80106 ( 80) hydrogen bonds : bond 0.03734 ( 1383) hydrogen bonds : angle 4.86354 ( 3975) link_BETA1-4 : bond 0.00490 ( 13) link_BETA1-4 : angle 2.27906 ( 39) link_NAG-ASN : bond 0.00392 ( 13) link_NAG-ASN : angle 4.51624 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 201 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 PHE cc_start: -0.0010 (m-10) cc_final: -0.0422 (m-10) REVERT: B 28 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7274 (t80) REVERT: B 389 ASP cc_start: 0.6558 (OUTLIER) cc_final: 0.5853 (m-30) REVERT: B 654 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: B 1142 GLN cc_start: 0.8660 (mm110) cc_final: 0.8367 (mm-40) REVERT: C 489 TYR cc_start: 0.3044 (OUTLIER) cc_final: 0.2472 (m-80) REVERT: C 902 MET cc_start: 0.9213 (tpt) cc_final: 0.8956 (tpt) REVERT: D 580 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.7644 (mp10) REVERT: D 850 ILE cc_start: -0.0349 (OUTLIER) cc_final: -0.0626 (mm) REVERT: D 981 LEU cc_start: 0.8358 (mt) cc_final: 0.8052 (mt) REVERT: E 69 TRP cc_start: 0.3950 (OUTLIER) cc_final: 0.3578 (t60) REVERT: E 284 PHE cc_start: 0.0335 (OUTLIER) cc_final: 0.0071 (t80) REVERT: E 556 MET cc_start: 0.2838 (tpt) cc_final: 0.2469 (tpt) outliers start: 129 outliers final: 100 residues processed: 320 average time/residue: 0.1917 time to fit residues: 105.9980 Evaluate side-chains 296 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 188 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 547 THR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 327 TRP Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 487 VAL Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 522 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 270 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 281 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 342 optimal weight: 0.0070 chunk 324 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 chunk 357 optimal weight: 3.9990 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 239 GLN ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.170070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120866 restraints weight = 81046.675| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.72 r_work: 0.3443 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36022 Z= 0.132 Angle : 0.602 14.399 49044 Z= 0.298 Chirality : 0.045 0.640 5475 Planarity : 0.004 0.058 6272 Dihedral : 4.790 38.475 5249 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.47 % Favored : 93.42 % Rotamer: Outliers : 3.08 % Allowed : 28.65 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 4344 helix: 1.30 (0.14), residues: 1443 sheet: -0.81 (0.21), residues: 582 loop : -1.53 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D1039 TYR 0.019 0.001 TYR E 384 PHE 0.029 0.001 PHE D 592 TRP 0.013 0.001 TRP A 476 HIS 0.004 0.001 HIS A 525 Details of bonding type rmsd covalent geometry : bond 0.00303 (35956) covalent geometry : angle 0.58349 (48886) SS BOND : bond 0.00393 ( 40) SS BOND : angle 1.62359 ( 80) hydrogen bonds : bond 0.03601 ( 1383) hydrogen bonds : angle 4.76734 ( 3975) link_BETA1-4 : bond 0.00463 ( 13) link_BETA1-4 : angle 2.19258 ( 39) link_NAG-ASN : bond 0.00409 ( 13) link_NAG-ASN : angle 4.41166 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8688 Ramachandran restraints generated. 4344 Oldfield, 0 Emsley, 4344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 198 time to evaluate : 1.353 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 463 PHE cc_start: -0.0106 (m-10) cc_final: -0.0502 (m-10) REVERT: B 28 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 389 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6049 (m-30) REVERT: B 654 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8359 (pt0) REVERT: B 740 MET cc_start: 0.8582 (mmm) cc_final: 0.8292 (mmm) REVERT: B 1142 GLN cc_start: 0.8617 (mm110) cc_final: 0.8311 (mm-40) REVERT: C 489 TYR cc_start: 0.2930 (OUTLIER) cc_final: 0.2317 (m-80) REVERT: D 580 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: D 850 ILE cc_start: -0.0300 (OUTLIER) cc_final: -0.0578 (mm) REVERT: D 981 LEU cc_start: 0.8307 (mt) cc_final: 0.8038 (mt) REVERT: E 69 TRP cc_start: 0.3977 (OUTLIER) cc_final: 0.3592 (t60) REVERT: E 191 ARG cc_start: 0.2862 (tpt170) cc_final: 0.2558 (mtp180) REVERT: E 284 PHE cc_start: 0.0330 (OUTLIER) cc_final: 0.0032 (t80) REVERT: E 382 MET cc_start: 0.4820 (ptm) cc_final: 0.3200 (mmt) REVERT: E 416 TYR cc_start: 0.2572 (t80) cc_final: 0.1783 (t80) REVERT: E 556 MET cc_start: 0.2863 (tpt) cc_final: 0.2540 (tpt) outliers start: 118 outliers final: 103 residues processed: 307 average time/residue: 0.1882 time to fit residues: 99.8200 Evaluate side-chains 300 residues out of total 3833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 189 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 296 MET Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain A residue 610 THR Chi-restraints excluded: chain B residue 28 TYR Chi-restraints excluded: chain B residue 64 TRP Chi-restraints excluded: chain B residue 113 LYS Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 492 LEU Chi-restraints excluded: chain D residue 511 VAL Chi-restraints excluded: chain D residue 515 PHE Chi-restraints excluded: chain D residue 534 VAL Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain D residue 662 CYS Chi-restraints excluded: chain D residue 760 CYS Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 866 THR Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1122 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 69 TRP Chi-restraints excluded: chain E residue 273 PHE Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain E residue 327 TRP Chi-restraints excluded: chain E residue 365 MET Chi-restraints excluded: chain E residue 375 MET Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 522 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 179 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 99 optimal weight: 0.0060 chunk 424 optimal weight: 0.4980 chunk 432 optimal weight: 6.9990 chunk 282 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 overall best weight: 2.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1074 ASN D 321 GLN ** D 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 220 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 = 0.4427 r_free = 0.4427 target = 0.167377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.117200 restraints weight = 79447.552| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.20 r_work: 0.3389 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 36022 Z= 0.238 Angle : 0.670 14.563 49044 Z= 0.334 Chirality : 0.047 0.670 5475 Planarity : 0.004 0.056 6272 Dihedral : 5.025 36.823 5249 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 3.24 % Allowed : 28.47 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.13), residues: 4344 helix: 1.16 (0.14), residues: 1439 sheet: -0.97 (0.21), residues: 582 loop : -1.62 (0.13), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1039 TYR 0.022 0.002 TYR C 265 PHE 0.028 0.002 PHE D 592 TRP 0.017 0.002 TRP A 476 HIS 0.010 0.001 HIS E 240 Details of bonding type rmsd covalent geometry : bond 0.00551 (35956) covalent geometry : angle 0.64845 (48886) SS BOND : bond 0.00459 ( 40) SS BOND : angle 1.99185 ( 80) hydrogen bonds : bond 0.03943 ( 1383) hydrogen bonds : angle 4.93607 ( 3975) link_BETA1-4 : bond 0.00336 ( 13) link_BETA1-4 : angle 2.29867 ( 39) link_NAG-ASN : bond 0.00539 ( 13) link_NAG-ASN : angle 4.81556 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11184.44 seconds wall clock time: 192 minutes 11.39 seconds (11531.39 seconds total)