Starting phenix.real_space_refine on Sun Sep 13 22:49:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.cif" model { file = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crx_7575/09_2026/6crx_7575.map" } resolution = 3.9 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= -0.000 sd= 0.007 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 138 5.16 5 C 16550 2.51 5 N 4197 2.21 5 O 5127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 33 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8346 Classifications: {'peptide': 1069} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1015} Chain breaks: 6 Chain: "A" Number of atoms: 8327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8327 Classifications: {'peptide': 1066} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1012} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.99, per 1000 atoms: 0.23 Number of scatterers: 26012 At special positions: 0 Unit cell: (150.38, 146.26, 187.46, 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 138 16.00 O 5127 8.00 N 4197 7.00 C 16550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.02 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.04 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.00 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.00 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.01 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.04 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.04 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.01 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.00 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.04 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA X 3 " - " MAN X 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG B1308 " - " ASN B 589 " " NAG B1309 " - " ASN B 691 " " NAG B1314 " - " ASN B1056 " " NAG B1317 " - " ASN B1116 " " NAG C1307 " - " ASN C 589 " " NAG C1312 " - " ASN C 691 " " NAG D 1 " - " ASN B 602 " " NAG E 1 " - " ASN B 65 " " NAG F 1 " - " ASN B 269 " " NAG G 1 " - " ASN B 783 " " NAG H 1 " - " ASN B1080 " " NAG I 1 " - " ASN B 318 " " NAG J 1 " - " ASN B 699 " " NAG K 1 " - " ASN C 65 " " NAG L 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 318 " " NAG N 1 " - " ASN C 602 " " NAG O 1 " - " ASN C 699 " " NAG P 1 " - " ASN C 783 " " NAG Q 1 " - " ASN C1056 " " NAG R 1 " - " ASN C1080 " " NAG S 1 " - " ASN C1116 " " NAG T 1 " - " ASN C 269 " " NAG U 1 " - " ASN A 269 " " NAG V 1 " - " ASN A 318 " " NAG W 1 " - " ASN A 589 " " NAG X 1 " - " ASN A 602 " " NAG Y 1 " - " ASN A 691 " " NAG Z 1 " - " ASN A 699 " " NAG a 1 " - " ASN A 783 " " NAG b 1 " - " ASN A1056 " " NAG c 1 " - " ASN A1080 " " NAG d 1 " - " ASN A1116 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 49 sheets defined 23.4% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 328 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.631A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.606A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.654A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 4.233A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 488 through 491 removed outlier: 3.767A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.900A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.946A pdb=" N LEU B 734 " --> pdb=" O GLU B 730 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 741 through 765 removed outlier: 3.557A pdb=" N LEU B 745 " --> pdb=" O PHE B 741 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 756 " --> pdb=" O ILE B 752 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 798 through 806 Processing helix chain 'B' and resid 848 through 864 removed outlier: 3.502A pdb=" N ILE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 872 removed outlier: 3.555A pdb=" N THR B 869 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 891 Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.757A pdb=" N ILE B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 4.296A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 removed outlier: 3.797A pdb=" N LEU B 966 " --> pdb=" O ILE B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 1016 removed outlier: 3.556A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 991 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.786A pdb=" N LEU C 286 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 391 through 395 removed outlier: 3.949A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 395' Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.903A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 491 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.695A pdb=" N LEU C 734 " --> pdb=" O GLU C 730 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.940A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 760 " --> pdb=" O GLN C 756 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 809 removed outlier: 3.727A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR C 809 " --> pdb=" O PHE C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 868 through 873 removed outlier: 3.771A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 903 through 923 removed outlier: 3.694A pdb=" N PHE C 909 " --> pdb=" O ILE C 905 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR C 923 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.624A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C 940 " --> pdb=" O GLN C 936 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 947 " --> pdb=" O THR C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1014 removed outlier: 3.527A pdb=" N SER C 985 " --> pdb=" O GLY C 981 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.579A pdb=" N ALA A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 336 through 340' Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.353A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 3.890A pdb=" N ASP A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.764A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.737A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 725 Processing helix chain 'A' and resid 729 through 736 removed outlier: 3.980A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 4.044A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 848 through 867 removed outlier: 3.891A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 removed outlier: 4.247A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.557A pdb=" N ARG A 887 " --> pdb=" O GLN A 883 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 891 " --> pdb=" O ARG A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.505A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.716A pdb=" N ASN A 937 " --> pdb=" O VAL A 933 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 removed outlier: 3.688A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.556A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A1011 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 removed outlier: 8.731A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 67 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 250 " --> pdb=" O THR B 71 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR B 92 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47 removed outlier: 6.215A pdb=" N PHE B 47 " --> pdb=" O ARG A 553 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 534 " --> pdb=" O PHE A 527 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.628A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 3.640A pdb=" N GLY B 104 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 82 removed outlier: 14.117A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 13.710A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.166A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU B 131 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE B 157 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS B 133 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N ASN B 155 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 11.397A pdb=" N ASN B 135 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N PHE B 153 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 149 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER B 141 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLN B 147 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 615 through 616 removed outlier: 4.577A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.449A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.729A pdb=" N LYS B 343 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 383 " --> pdb=" O SER B 500 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 500 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 498 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 497 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU B 421 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.776A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'B' and resid 640 through 646 removed outlier: 4.938A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 677 " --> pdb=" O CYS B 657 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.283A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 693 through 700 removed outlier: 6.809A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 703 through 709 removed outlier: 3.640A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B1038 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AB7, first strand: chain 'B' and resid 769 through 771 Processing sheet with id=AB8, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AB9, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 3.603A pdb=" N SER B1105 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ALA B1069 " --> pdb=" O SER B1105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.536A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS C 180 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 52 through 59 removed outlier: 7.516A pdb=" N THR C 261 " --> pdb=" O ASP C 277 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 277 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C 263 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 275 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 265 " --> pdb=" O THR C 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.598A pdb=" N ARG C 232 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.679A pdb=" N PHE C 231 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 12.465A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 12.362A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 9.370A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C 123 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR C 163 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE C 125 " --> pdb=" O PHE C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE C 161 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA C 127 " --> pdb=" O CYS C 159 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS C 159 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 157 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 131 " --> pdb=" O ASN C 155 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN C 155 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N CYS C 133 " --> pdb=" O PHE C 153 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N PHE C 153 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASN C 135 " --> pdb=" O MET C 151 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N MET C 151 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE C 137 " --> pdb=" O HIS C 149 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N HIS C 149 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 147 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 615 through 616 removed outlier: 4.019A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 312 through 314 removed outlier: 6.591A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE C 551 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 344 through 345 removed outlier: 3.699A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 385 through 390 removed outlier: 3.529A pdb=" N PHE C 387 " --> pdb=" O VAL C 496 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AD1, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.245A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 683 through 685 removed outlier: 5.630A pdb=" N ALA C 683 " --> pdb=" O MET A 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.725A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AD6, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AD7, first strand: chain 'C' and resid 821 through 823 removed outlier: 3.537A pdb=" N GLU C 821 " --> pdb=" O ALA C 834 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 834 " --> pdb=" O GLU C 821 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 5.164A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.764A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.592A pdb=" N THR A 51 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.571A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.612A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN A 135 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A 152 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE A 137 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR A 150 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AE4, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.438A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.574A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 421 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LEU A 499 " --> pdb=" O CYS A 419 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.557A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AE8, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.140A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 677 " --> pdb=" O CYS A 657 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.577A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 707 " --> pdb=" O PHE A1044 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 1029 through 1033 removed outlier: 6.904A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AF3, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AF4, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 4.782A pdb=" N VAL A1104 " --> pdb=" O PHE A1071 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N PHE A1071 " --> pdb=" O VAL A1104 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY A1106 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A1065 " --> pdb=" O LYS A1068 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2562 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.99 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8118 1.34 - 1.47: 7104 1.47 - 1.59: 11201 1.59 - 1.72: 0 1.72 - 1.85: 186 Bond restraints: 26609 Sorted by residual: bond pdb=" C1 MAN X 4 " pdb=" O5 MAN X 4 " ideal model delta sigma weight residual 1.399 1.470 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C TYR C1070 " pdb=" N PHE C1071 " ideal model delta sigma weight residual 1.331 1.261 0.070 2.07e-02 2.33e+03 1.13e+01 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C ILE A 573 " pdb=" N SER A 574 " ideal model delta sigma weight residual 1.327 1.270 0.057 1.71e-02 3.42e+03 1.11e+01 bond pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sigma weight residual 1.417 1.481 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 26604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 35056 2.78 - 5.56: 1012 5.56 - 8.34: 119 8.34 - 11.12: 14 11.12 - 13.90: 3 Bond angle restraints: 36204 Sorted by residual: angle pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 908 " pdb=" N PHE C 909 " pdb=" CA PHE C 909 " ideal model delta sigma weight residual 122.06 112.43 9.63 1.86e+00 2.89e-01 2.68e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C ILE A 72 " pdb=" N ASN A 73 " pdb=" CA ASN A 73 " ideal model delta sigma weight residual 120.82 127.95 -7.13 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C THR B 106 " pdb=" N MET B 107 " pdb=" CA MET B 107 " ideal model delta sigma weight residual 121.54 130.21 -8.67 1.91e+00 2.74e-01 2.06e+01 ... (remaining 36199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 14612 17.43 - 34.85: 503 34.85 - 52.28: 107 52.28 - 69.70: 9 69.70 - 87.13: 7 Dihedral angle restraints: 15238 sinusoidal: 5907 harmonic: 9331 Sorted by residual: dihedral pdb=" CB CYS B1014 " pdb=" SG CYS B1014 " pdb=" SG CYS B1025 " pdb=" CB CYS B1025 " ideal model delta sinusoidal sigma weight residual -86.00 -173.13 87.13 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA PHE A 83 " pdb=" C PHE A 83 " pdb=" N LYS A 84 " pdb=" CA LYS A 84 " ideal model delta harmonic sigma weight residual -180.00 -133.37 -46.63 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA SER A 35 " pdb=" C SER A 35 " pdb=" N SER A 36 " pdb=" CA SER A 36 " ideal model delta harmonic sigma weight residual -180.00 -134.27 -45.73 0 5.00e+00 4.00e-02 8.36e+01 ... (remaining 15235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 4099 0.122 - 0.243: 181 0.243 - 0.365: 19 0.365 - 0.486: 1 0.486 - 0.608: 2 Chirality restraints: 4302 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN A 691 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN C1116 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN A 783 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.30e+00 ... (remaining 4299 not shown) Planarity restraints: 4609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PHE A 83 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 968 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO B 969 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 969 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 969 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 380 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C SER C 380 " 0.055 2.00e-02 2.50e+03 pdb=" O SER C 380 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 381 " -0.019 2.00e-02 2.50e+03 ... (remaining 4606 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3580 2.75 - 3.28: 24044 3.28 - 3.82: 43698 3.82 - 4.36: 50954 4.36 - 4.90: 85587 Nonbonded interactions: 207863 Sorted by model distance: nonbonded pdb=" O GLY B 77 " pdb=" OH TYR B 252 " model vdw 2.208 3.040 nonbonded pdb=" O PHE B1071 " pdb=" OG1 THR B1102 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLN A 947 " pdb=" OG SER A 985 " model vdw 2.231 3.040 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR C 41 " pdb=" O LEU C 58 " model vdw 2.249 3.040 ... (remaining 207858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1308)) selection = (chain 'C' and (resid 18 through 662 or resid 672 through 823 or resid 832 throu \ gh 1307)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'N' selection = chain 'O' selection = chain 'X' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.920 Find NCS groups from input model: 0.900 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: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.010 0.115 26728 Z= 0.456 Angle : 1.149 13.902 36516 Z= 0.598 Chirality : 0.064 0.608 4302 Planarity : 0.007 0.083 4575 Dihedral : 9.421 72.342 9101 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 0.18 % Allowed : 1.12 % Favored : 98.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.12), residues: 3161 helix: -3.72 (0.12), residues: 648 sheet: -1.17 (0.20), residues: 606 loop : -2.57 (0.12), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 453 TYR 0.043 0.004 TYR B1029 PHE 0.043 0.005 PHE B 22 TRP 0.026 0.004 TRP C 340 HIS 0.018 0.004 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.01003 / 0.46 (26609) covalent geometry : angle 1.11752 / 0.59 (36204) SS BOND : bond 0.01081 / 0.73 ( 45) SS BOND : angle 2.12689 / 1.37 ( 90) hydrogen bonds : bond 0.28537 / 19.12 ( 900) hydrogen bonds : angle 10.73853 / 7.29 ( 2562) link_ALPHA1-3 : bond 0.00689 / 0.38 ( 5) link_ALPHA1-3 : angle 2.19063 / 1.50 ( 15) link_BETA1-4 : bond 0.00796 / 0.57 ( 35) link_BETA1-4 : angle 3.28140 / 2.21 ( 105) link_NAG-ASN : bond 0.01046 / 0.68 ( 34) link_NAG-ASN : angle 3.69464 / 2.53 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 370 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 THR cc_start: 0.5041 (m) cc_final: 0.4605 (t) REVERT: B 103 PHE cc_start: 0.8578 (m-80) cc_final: 0.8282 (m-10) REVERT: B 107 MET cc_start: 0.4623 (mmt) cc_final: 0.3682 (mmt) REVERT: B 155 ASN cc_start: 0.8350 (m-40) cc_final: 0.7951 (m110) REVERT: B 194 LEU cc_start: 0.8287 (tp) cc_final: 0.7781 (tt) REVERT: B 1099 THR cc_start: 0.8326 (p) cc_final: 0.8113 (t) REVERT: C 50 ASP cc_start: 0.8092 (t0) cc_final: 0.7685 (t0) REVERT: C 407 ASP cc_start: 0.6412 (m-30) cc_final: 0.5356 (p0) REVERT: C 709 MET cc_start: 0.8384 (mtm) cc_final: 0.8115 (mmm) REVERT: C 884 MET cc_start: 0.8343 (mmm) cc_final: 0.8025 (mmm) REVERT: C 886 TYR cc_start: 0.7351 (t80) cc_final: 0.7058 (t80) REVERT: A 87 ILE cc_start: 0.9046 (pt) cc_final: 0.8389 (mm) REVERT: A 606 VAL cc_start: 0.8793 (t) cc_final: 0.8488 (t) REVERT: A 939 GLN cc_start: 0.7863 (mt0) cc_final: 0.7611 (tm-30) outliers start: 5 outliers final: 0 residues processed: 375 average time/residue: 0.1788 time to fit residues: 103.7939 Evaluate side-chains 178 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 29 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 ASN B 993 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN C 29 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 396 GLN C 445 HIS C 530 ASN C 786 GLN C 838 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 937 ASN C 993 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 733 ASN ** A 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 GLN A 889 ASN A 896 ASN A1030 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.119255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.090784 restraints weight = 107332.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.090724 restraints weight = 75989.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091093 restraints weight = 59228.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091482 restraints weight = 54923.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091632 restraints weight = 47288.636| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 26728 Z= 0.193 Angle : 0.751 10.306 36516 Z= 0.389 Chirality : 0.047 0.236 4302 Planarity : 0.005 0.066 4575 Dihedral : 6.232 36.591 3437 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.44 % Allowed : 7.20 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.58 (0.13), residues: 3161 helix: -1.43 (0.17), residues: 661 sheet: -1.00 (0.19), residues: 637 loop : -2.15 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 620 TYR 0.020 0.002 TYR B 481 PHE 0.027 0.002 PHE B 325 TRP 0.013 0.002 TRP C 423 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (26609) covalent geometry : angle 0.73270 / 0.39 (36204) SS BOND : bond 0.00485 / 0.31 ( 45) SS BOND : angle 1.54986 / 0.98 ( 90) hydrogen bonds : bond 0.06185 / 4.17 ( 900) hydrogen bonds : angle 6.86431 / 4.67 ( 2562) link_ALPHA1-3 : bond 0.00777 / 0.39 ( 5) link_ALPHA1-3 : angle 1.80754 / 1.21 ( 15) link_BETA1-4 : bond 0.00549 / 0.36 ( 35) link_BETA1-4 : angle 2.00455 / 1.47 ( 105) link_NAG-ASN : bond 0.00415 / 0.28 ( 34) link_NAG-ASN : angle 2.19892 / 1.52 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 221 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6682 (OUTLIER) cc_final: 0.6135 (mp) REVERT: B 87 ILE cc_start: 0.8695 (tt) cc_final: 0.8058 (mm) REVERT: B 103 PHE cc_start: 0.8576 (m-80) cc_final: 0.8344 (m-10) REVERT: B 107 MET cc_start: 0.4937 (mmt) cc_final: 0.4004 (mmt) REVERT: B 155 ASN cc_start: 0.8118 (m-40) cc_final: 0.7703 (m110) REVERT: B 164 ILE cc_start: 0.9359 (mt) cc_final: 0.9155 (tp) REVERT: B 194 LEU cc_start: 0.8357 (tp) cc_final: 0.8122 (tp) REVERT: B 231 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7226 (p90) REVERT: B 737 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7741 (mp10) REVERT: B 1099 THR cc_start: 0.8231 (p) cc_final: 0.7971 (t) REVERT: C 407 ASP cc_start: 0.6465 (m-30) cc_final: 0.5381 (p0) REVERT: C 707 GLU cc_start: 0.7267 (pt0) cc_final: 0.7010 (pt0) REVERT: C 884 MET cc_start: 0.8538 (mmm) cc_final: 0.8227 (mmm) REVERT: C 886 TYR cc_start: 0.7752 (t80) cc_final: 0.7479 (t80) REVERT: A 107 MET cc_start: 0.4222 (mmt) cc_final: 0.3956 (mmt) REVERT: A 150 THR cc_start: 0.0873 (OUTLIER) cc_final: 0.0545 (t) REVERT: A 151 MET cc_start: 0.4964 (mmm) cc_final: 0.3860 (mtp) REVERT: A 288 CYS cc_start: 0.6510 (m) cc_final: 0.6217 (m) REVERT: A 939 GLN cc_start: 0.7858 (mt0) cc_final: 0.7552 (tm-30) REVERT: A 942 ASN cc_start: 0.8519 (t0) cc_final: 0.8310 (t0) outliers start: 40 outliers final: 19 residues processed: 251 average time/residue: 0.1507 time to fit residues: 62.9709 Evaluate side-chains 182 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 757 ASP Chi-restraints excluded: chain B residue 896 ASN Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 143 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 149 optimal weight: 50.0000 chunk 277 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1090 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 661 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 902 GLN C1005 ASN A 135 ASN A 632 GLN A 786 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.115336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088555 restraints weight = 109052.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.088061 restraints weight = 77846.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088275 restraints weight = 61767.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088560 restraints weight = 58809.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.088786 restraints weight = 49963.953| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 26728 Z= 0.245 Angle : 0.764 9.817 36516 Z= 0.388 Chirality : 0.048 0.220 4302 Planarity : 0.005 0.060 4575 Dihedral : 5.949 32.329 3437 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.20 % Allowed : 8.78 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.21 (0.14), residues: 3161 helix: -0.39 (0.19), residues: 649 sheet: -1.13 (0.20), residues: 627 loop : -2.06 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 453 TYR 0.020 0.002 TYR B 855 PHE 0.026 0.002 PHE C 83 TRP 0.017 0.002 TRP C 423 HIS 0.008 0.002 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.24 (26609) covalent geometry : angle 0.74723 / 0.38 (36204) SS BOND : bond 0.00505 / 0.37 ( 45) SS BOND : angle 1.44293 / 0.92 ( 90) hydrogen bonds : bond 0.05471 / 3.69 ( 900) hydrogen bonds : angle 6.48977 / 4.42 ( 2562) link_ALPHA1-3 : bond 0.00636 / 0.32 ( 5) link_ALPHA1-3 : angle 1.72422 / 1.17 ( 15) link_BETA1-4 : bond 0.00467 / 0.31 ( 35) link_BETA1-4 : angle 1.98071 / 1.41 ( 105) link_NAG-ASN : bond 0.00546 / 0.35 ( 34) link_NAG-ASN : angle 2.17571 / 1.47 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6642 (OUTLIER) cc_final: 0.6152 (mp) REVERT: B 87 ILE cc_start: 0.8782 (tt) cc_final: 0.8185 (mm) REVERT: B 107 MET cc_start: 0.4907 (mmt) cc_final: 0.3630 (mmm) REVERT: B 155 ASN cc_start: 0.8143 (m-40) cc_final: 0.7737 (m110) REVERT: B 231 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6976 (p90) REVERT: B 600 ASP cc_start: 0.7189 (t70) cc_final: 0.6803 (t70) REVERT: B 1099 THR cc_start: 0.8350 (p) cc_final: 0.8062 (t) REVERT: C 407 ASP cc_start: 0.6222 (m-30) cc_final: 0.5141 (p0) REVERT: C 886 TYR cc_start: 0.7883 (t80) cc_final: 0.7606 (t80) REVERT: C 961 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8131 (p0) REVERT: A 939 GLN cc_start: 0.7906 (mt0) cc_final: 0.7643 (tm-30) REVERT: A 942 ASN cc_start: 0.8647 (t0) cc_final: 0.8382 (t0) outliers start: 61 outliers final: 36 residues processed: 215 average time/residue: 0.1407 time to fit residues: 52.1289 Evaluate side-chains 191 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 961 ASP Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain C residue 991 THR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 186 optimal weight: 0.9980 chunk 263 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 284 optimal weight: 0.4980 chunk 162 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 151 optimal weight: 50.0000 chunk 36 optimal weight: 0.0870 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 248 optimal weight: 40.0000 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 641 HIS ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN B 907 ASN B1036 GLN C 158 ASN C 661 HIS ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 902 GLN C1036 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.118255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091289 restraints weight = 107713.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091571 restraints weight = 73089.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.091201 restraints weight = 58016.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091461 restraints weight = 59079.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.092373 restraints weight = 50926.056| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26728 Z= 0.117 Angle : 0.624 13.333 36516 Z= 0.316 Chirality : 0.045 0.222 4302 Planarity : 0.004 0.058 4575 Dihedral : 5.270 28.911 3437 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.26 % Allowed : 10.80 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.71 (0.14), residues: 3161 helix: 0.31 (0.20), residues: 658 sheet: -0.72 (0.21), residues: 595 loop : -1.89 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 620 TYR 0.021 0.001 TYR A 886 PHE 0.024 0.001 PHE C 83 TRP 0.015 0.001 TRP C 423 HIS 0.003 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (26609) covalent geometry : angle 0.61059 / 0.31 (36204) SS BOND : bond 0.00636 / 0.42 ( 45) SS BOND : angle 1.18164 / 0.75 ( 90) hydrogen bonds : bond 0.04369 / 2.94 ( 900) hydrogen bonds : angle 5.82876 / 3.97 ( 2562) link_ALPHA1-3 : bond 0.00792 / 0.40 ( 5) link_ALPHA1-3 : angle 1.61318 / 1.14 ( 15) link_BETA1-4 : bond 0.00386 / 0.26 ( 35) link_BETA1-4 : angle 1.62013 / 1.17 ( 105) link_NAG-ASN : bond 0.00294 / 0.21 ( 34) link_NAG-ASN : angle 1.63018 / 1.11 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 CYS cc_start: 0.5006 (OUTLIER) cc_final: 0.3816 (t) REVERT: B 81 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6155 (mp) REVERT: B 87 ILE cc_start: 0.8704 (tt) cc_final: 0.8098 (mm) REVERT: B 107 MET cc_start: 0.4514 (mmt) cc_final: 0.4100 (mmt) REVERT: B 155 ASN cc_start: 0.8050 (m-40) cc_final: 0.7642 (m110) REVERT: B 231 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7128 (p90) REVERT: B 600 ASP cc_start: 0.6846 (t70) cc_final: 0.6282 (t70) REVERT: B 1099 THR cc_start: 0.8181 (p) cc_final: 0.7927 (t) REVERT: C 407 ASP cc_start: 0.6397 (m-30) cc_final: 0.5364 (p0) REVERT: C 884 MET cc_start: 0.8441 (mmm) cc_final: 0.8090 (mmm) REVERT: C 886 TYR cc_start: 0.7823 (t80) cc_final: 0.7541 (t80) REVERT: A 37 MET cc_start: 0.8138 (mtm) cc_final: 0.7775 (mpp) REVERT: A 150 THR cc_start: 0.1097 (OUTLIER) cc_final: 0.0827 (t) REVERT: A 151 MET cc_start: 0.5295 (mmm) cc_final: 0.4184 (tmm) REVERT: A 413 PRO cc_start: 0.5168 (Cg_endo) cc_final: 0.4837 (Cg_exo) REVERT: A 942 ASN cc_start: 0.8537 (t0) cc_final: 0.8271 (t0) outliers start: 35 outliers final: 14 residues processed: 219 average time/residue: 0.1399 time to fit residues: 53.1542 Evaluate side-chains 180 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1110 VAL Chi-restraints excluded: chain A residue 1114 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 312 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 301 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.0670 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 947 GLN C 118 ASN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 627 ASN A 661 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.118294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091356 restraints weight = 107072.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091360 restraints weight = 71772.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.091333 restraints weight = 59022.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.091743 restraints weight = 57602.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.091803 restraints weight = 48455.794| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26728 Z= 0.115 Angle : 0.602 12.747 36516 Z= 0.303 Chirality : 0.044 0.203 4302 Planarity : 0.004 0.055 4575 Dihedral : 5.008 29.125 3437 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.44 % Allowed : 11.51 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.51 (0.14), residues: 3161 helix: 0.74 (0.21), residues: 655 sheet: -0.70 (0.20), residues: 617 loop : -1.83 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1073 TYR 0.014 0.001 TYR B 723 PHE 0.024 0.001 PHE A 360 TRP 0.016 0.001 TRP C 423 HIS 0.003 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (26609) covalent geometry : angle 0.58939 / 0.30 (36204) SS BOND : bond 0.00488 / 0.32 ( 45) SS BOND : angle 1.07501 / 0.78 ( 90) hydrogen bonds : bond 0.04095 / 2.76 ( 900) hydrogen bonds : angle 5.62749 / 3.84 ( 2562) link_ALPHA1-3 : bond 0.00672 / 0.34 ( 5) link_ALPHA1-3 : angle 1.56871 / 1.10 ( 15) link_BETA1-4 : bond 0.00375 / 0.25 ( 35) link_BETA1-4 : angle 1.60516 / 1.16 ( 105) link_NAG-ASN : bond 0.00241 / 0.17 ( 34) link_NAG-ASN : angle 1.49085 / 1.02 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 CYS cc_start: 0.4696 (OUTLIER) cc_final: 0.3527 (t) REVERT: B 81 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.6056 (mp) REVERT: B 87 ILE cc_start: 0.8720 (tt) cc_final: 0.8087 (mm) REVERT: B 107 MET cc_start: 0.4489 (mmt) cc_final: 0.4043 (mmt) REVERT: B 155 ASN cc_start: 0.8089 (m-40) cc_final: 0.7696 (m110) REVERT: B 217 LYS cc_start: 0.9086 (mttt) cc_final: 0.8749 (mppt) REVERT: B 231 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7155 (p90) REVERT: B 600 ASP cc_start: 0.6775 (t70) cc_final: 0.6125 (t70) REVERT: B 1099 THR cc_start: 0.8172 (p) cc_final: 0.7892 (t) REVERT: C 407 ASP cc_start: 0.6335 (m-30) cc_final: 0.5329 (p0) REVERT: C 417 MET cc_start: 0.2272 (tpt) cc_final: -0.2034 (ptm) REVERT: C 886 TYR cc_start: 0.7809 (t80) cc_final: 0.7571 (t80) REVERT: A 37 MET cc_start: 0.8051 (mtm) cc_final: 0.7789 (mpp) REVERT: A 150 THR cc_start: 0.1095 (OUTLIER) cc_final: 0.0830 (t) REVERT: A 151 MET cc_start: 0.5291 (mmm) cc_final: 0.3840 (tmm) REVERT: A 713 MET cc_start: 0.8789 (ptm) cc_final: 0.8430 (ptm) REVERT: A 942 ASN cc_start: 0.8626 (t0) cc_final: 0.8387 (t0) outliers start: 40 outliers final: 23 residues processed: 217 average time/residue: 0.1438 time to fit residues: 53.1963 Evaluate side-chains 189 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1009 THR Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 233 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 201 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 219 optimal weight: 20.0000 chunk 181 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 ASN B 907 ASN B 947 GLN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 ASN A 733 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.115504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.088641 restraints weight = 108270.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.087747 restraints weight = 84827.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.087502 restraints weight = 70311.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.087856 restraints weight = 73370.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.088075 restraints weight = 59045.628| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26728 Z= 0.215 Angle : 0.701 12.596 36516 Z= 0.352 Chirality : 0.046 0.212 4302 Planarity : 0.005 0.057 4575 Dihedral : 5.231 31.728 3437 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.23 % Allowed : 12.16 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3161 helix: 0.47 (0.20), residues: 656 sheet: -0.84 (0.21), residues: 607 loop : -1.88 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1073 TYR 0.020 0.002 TYR A 300 PHE 0.025 0.002 PHE C 83 TRP 0.015 0.002 TRP C 423 HIS 0.006 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (26609) covalent geometry : angle 0.68696 / 0.35 (36204) SS BOND : bond 0.00406 / 0.28 ( 45) SS BOND : angle 1.28679 / 0.85 ( 90) hydrogen bonds : bond 0.04621 / 3.12 ( 900) hydrogen bonds : angle 5.88282 / 4.02 ( 2562) link_ALPHA1-3 : bond 0.00667 / 0.33 ( 5) link_ALPHA1-3 : angle 1.64581 / 1.13 ( 15) link_BETA1-4 : bond 0.00433 / 0.29 ( 35) link_BETA1-4 : angle 1.80484 / 1.30 ( 105) link_NAG-ASN : bond 0.00458 / 0.30 ( 34) link_NAG-ASN : angle 1.81228 / 1.22 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 155 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6447 (mm) cc_final: 0.6020 (mp) REVERT: B 87 ILE cc_start: 0.8771 (tt) cc_final: 0.8197 (mm) REVERT: B 107 MET cc_start: 0.5255 (mmt) cc_final: 0.4742 (mmt) REVERT: B 155 ASN cc_start: 0.8207 (m-40) cc_final: 0.7826 (m110) REVERT: B 231 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7219 (p90) REVERT: B 600 ASP cc_start: 0.7144 (t70) cc_final: 0.6569 (t70) REVERT: B 984 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7319 (tm-30) REVERT: B 1099 THR cc_start: 0.8399 (p) cc_final: 0.8128 (t) REVERT: C 407 ASP cc_start: 0.6407 (m-30) cc_final: 0.5241 (p0) REVERT: C 417 MET cc_start: 0.2447 (tpt) cc_final: -0.2100 (ptm) REVERT: C 758 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8158 (ttt180) REVERT: C 886 TYR cc_start: 0.7980 (t80) cc_final: 0.7720 (t80) REVERT: A 37 MET cc_start: 0.8004 (mtm) cc_final: 0.7513 (mpp) REVERT: A 150 THR cc_start: 0.1432 (OUTLIER) cc_final: 0.1183 (t) REVERT: A 151 MET cc_start: 0.5333 (mmm) cc_final: 0.3972 (tmm) REVERT: A 364 PHE cc_start: 0.1709 (m-80) cc_final: 0.1302 (m-80) REVERT: A 799 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8435 (t80) REVERT: A 865 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.7972 (m) REVERT: A 942 ASN cc_start: 0.8663 (t0) cc_final: 0.8411 (t0) outliers start: 62 outliers final: 37 residues processed: 204 average time/residue: 0.1396 time to fit residues: 49.6430 Evaluate side-chains 194 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 22 optimal weight: 30.0000 chunk 287 optimal weight: 0.0870 chunk 101 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 271 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 chunk 307 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN A 766 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.117091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.090291 restraints weight = 107599.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.089773 restraints weight = 75362.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.090104 restraints weight = 64469.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.090243 restraints weight = 62264.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.090412 restraints weight = 51523.379| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26728 Z= 0.122 Angle : 0.602 13.862 36516 Z= 0.302 Chirality : 0.044 0.198 4302 Planarity : 0.004 0.059 4575 Dihedral : 4.911 29.357 3437 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.62 % Allowed : 12.85 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.42 (0.14), residues: 3161 helix: 0.96 (0.21), residues: 648 sheet: -0.58 (0.21), residues: 577 loop : -1.82 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1073 TYR 0.016 0.001 TYR C1049 PHE 0.024 0.001 PHE C 83 TRP 0.015 0.001 TRP B 868 HIS 0.003 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (26609) covalent geometry : angle 0.59018 / 0.30 (36204) SS BOND : bond 0.00316 / 0.20 ( 45) SS BOND : angle 1.00473 / 0.66 ( 90) hydrogen bonds : bond 0.04094 / 2.78 ( 900) hydrogen bonds : angle 5.53475 / 3.78 ( 2562) link_ALPHA1-3 : bond 0.00518 / 0.26 ( 5) link_ALPHA1-3 : angle 1.59309 / 1.14 ( 15) link_BETA1-4 : bond 0.00378 / 0.26 ( 35) link_BETA1-4 : angle 1.58607 / 1.13 ( 105) link_NAG-ASN : bond 0.00255 / 0.17 ( 34) link_NAG-ASN : angle 1.54917 / 1.05 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6456 (OUTLIER) cc_final: 0.6040 (mp) REVERT: B 87 ILE cc_start: 0.8720 (tt) cc_final: 0.8124 (mm) REVERT: B 107 MET cc_start: 0.4661 (mmt) cc_final: 0.4196 (mmt) REVERT: B 155 ASN cc_start: 0.7988 (m-40) cc_final: 0.7592 (m110) REVERT: B 231 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7207 (p90) REVERT: B 1099 THR cc_start: 0.8475 (p) cc_final: 0.8204 (t) REVERT: C 262 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: C 407 ASP cc_start: 0.6386 (m-30) cc_final: 0.5244 (p0) REVERT: C 417 MET cc_start: 0.2592 (tpt) cc_final: -0.1837 (ptm) REVERT: C 884 MET cc_start: 0.8348 (mmm) cc_final: 0.8052 (mmm) REVERT: C 886 TYR cc_start: 0.7915 (t80) cc_final: 0.7653 (t80) REVERT: A 37 MET cc_start: 0.8055 (mtm) cc_final: 0.7493 (mpp) REVERT: A 151 MET cc_start: 0.5789 (mmm) cc_final: 0.4377 (tmm) REVERT: A 312 ASP cc_start: 0.8169 (m-30) cc_final: 0.7906 (t0) REVERT: A 799 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8416 (t80) REVERT: A 865 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7891 (m) REVERT: A 942 ASN cc_start: 0.8683 (t0) cc_final: 0.8449 (t0) REVERT: A 970 GLU cc_start: 0.8347 (tp30) cc_final: 0.8119 (tp30) outliers start: 45 outliers final: 26 residues processed: 208 average time/residue: 0.1398 time to fit residues: 49.5536 Evaluate side-chains 193 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 999 GLU Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 231 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 290 optimal weight: 0.5980 chunk 55 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 212 optimal weight: 40.0000 chunk 291 optimal weight: 0.6980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 135 ASN ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** 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 = 0.4114 r_free = 0.4114 target = 0.115734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.089095 restraints weight = 108911.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.088688 restraints weight = 79293.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.088446 restraints weight = 70959.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089027 restraints weight = 63453.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089189 restraints weight = 53206.902| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26728 Z= 0.184 Angle : 0.661 13.843 36516 Z= 0.331 Chirality : 0.045 0.202 4302 Planarity : 0.004 0.064 4575 Dihedral : 5.016 31.292 3437 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 1.80 % Allowed : 13.03 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.14), residues: 3161 helix: 0.75 (0.20), residues: 654 sheet: -0.72 (0.21), residues: 602 loop : -1.84 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 758 TYR 0.014 0.001 TYR B 855 PHE 0.024 0.002 PHE C 83 TRP 0.014 0.001 TRP C 423 HIS 0.005 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (26609) covalent geometry : angle 0.64824 / 0.33 (36204) SS BOND : bond 0.00382 / 0.25 ( 45) SS BOND : angle 1.04696 / 0.69 ( 90) hydrogen bonds : bond 0.04374 / 2.97 ( 900) hydrogen bonds : angle 5.66144 / 3.87 ( 2562) link_ALPHA1-3 : bond 0.00536 / 0.27 ( 5) link_ALPHA1-3 : angle 1.62300 / 1.14 ( 15) link_BETA1-4 : bond 0.00396 / 0.27 ( 35) link_BETA1-4 : angle 1.71210 / 1.23 ( 105) link_NAG-ASN : bond 0.00376 / 0.25 ( 34) link_NAG-ASN : angle 1.70690 / 1.16 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 160 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6355 (OUTLIER) cc_final: 0.5996 (mp) REVERT: B 87 ILE cc_start: 0.8741 (tt) cc_final: 0.8152 (mm) REVERT: B 107 MET cc_start: 0.4926 (mmt) cc_final: 0.4505 (mmt) REVERT: B 155 ASN cc_start: 0.8057 (m-40) cc_final: 0.7711 (m110) REVERT: B 231 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7209 (p90) REVERT: B 1099 THR cc_start: 0.8521 (p) cc_final: 0.8246 (t) REVERT: C 262 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8713 (m-80) REVERT: C 407 ASP cc_start: 0.6478 (m-30) cc_final: 0.5210 (p0) REVERT: C 417 MET cc_start: 0.2527 (tpt) cc_final: -0.1929 (ptm) REVERT: C 758 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8135 (ttt180) REVERT: C 886 TYR cc_start: 0.7996 (t80) cc_final: 0.7734 (t80) REVERT: A 37 MET cc_start: 0.8071 (mtm) cc_final: 0.7518 (mpp) REVERT: A 151 MET cc_start: 0.5711 (mmm) cc_final: 0.4246 (tmm) REVERT: A 312 ASP cc_start: 0.8204 (m-30) cc_final: 0.7934 (t0) REVERT: A 799 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8418 (t80) REVERT: A 942 ASN cc_start: 0.8622 (t0) cc_final: 0.8378 (t0) REVERT: A 970 GLU cc_start: 0.8385 (tp30) cc_final: 0.8161 (tp30) outliers start: 50 outliers final: 29 residues processed: 199 average time/residue: 0.1455 time to fit residues: 49.6761 Evaluate side-chains 188 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 763 VAL Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 297 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 179 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 152 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 GLN ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.116481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.090000 restraints weight = 108407.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089504 restraints weight = 76714.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.089867 restraints weight = 62678.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.090083 restraints weight = 59821.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.090231 restraints weight = 52675.792| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26728 Z= 0.139 Angle : 0.622 13.943 36516 Z= 0.312 Chirality : 0.045 0.198 4302 Planarity : 0.004 0.064 4575 Dihedral : 4.890 29.655 3437 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.73 % Allowed : 13.10 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.43 (0.14), residues: 3161 helix: 0.95 (0.21), residues: 648 sheet: -0.60 (0.21), residues: 585 loop : -1.83 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1073 TYR 0.021 0.001 TYR C 300 PHE 0.024 0.001 PHE C 83 TRP 0.019 0.001 TRP A 423 HIS 0.004 0.001 HIS A 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (26609) covalent geometry : angle 0.61045 / 0.31 (36204) SS BOND : bond 0.00329 / 0.21 ( 45) SS BOND : angle 0.97163 / 0.64 ( 90) hydrogen bonds : bond 0.04131 / 2.80 ( 900) hydrogen bonds : angle 5.50254 / 3.76 ( 2562) link_ALPHA1-3 : bond 0.00630 / 0.32 ( 5) link_ALPHA1-3 : angle 1.60432 / 1.14 ( 15) link_BETA1-4 : bond 0.00390 / 0.26 ( 35) link_BETA1-4 : angle 1.59718 / 1.14 ( 105) link_NAG-ASN : bond 0.00272 / 0.18 ( 34) link_NAG-ASN : angle 1.58363 / 1.08 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 164 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ILE cc_start: 0.6437 (OUTLIER) cc_final: 0.6109 (mp) REVERT: B 87 ILE cc_start: 0.8716 (tt) cc_final: 0.8137 (mm) REVERT: B 107 MET cc_start: 0.4466 (mmt) cc_final: 0.3850 (mmt) REVERT: B 155 ASN cc_start: 0.8036 (m-40) cc_final: 0.7676 (m110) REVERT: B 231 PHE cc_start: 0.8084 (OUTLIER) cc_final: 0.7128 (p90) REVERT: B 1099 THR cc_start: 0.8483 (p) cc_final: 0.8203 (t) REVERT: C 37 MET cc_start: 0.7484 (mmm) cc_final: 0.7260 (mmm) REVERT: C 262 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8725 (m-80) REVERT: C 407 ASP cc_start: 0.6449 (m-30) cc_final: 0.5206 (p0) REVERT: C 417 MET cc_start: 0.2482 (tpt) cc_final: -0.1844 (ptm) REVERT: C 758 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8066 (ttt180) REVERT: C 886 TYR cc_start: 0.7980 (t80) cc_final: 0.7711 (t80) REVERT: A 37 MET cc_start: 0.8091 (mtm) cc_final: 0.7565 (mpp) REVERT: A 151 MET cc_start: 0.5397 (mmm) cc_final: 0.3888 (tmm) REVERT: A 197 TYR cc_start: 0.8112 (m-10) cc_final: 0.7904 (m-10) REVERT: A 312 ASP cc_start: 0.8122 (m-30) cc_final: 0.7870 (t0) REVERT: A 799 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8402 (t80) REVERT: A 942 ASN cc_start: 0.8622 (t0) cc_final: 0.8385 (t0) outliers start: 48 outliers final: 32 residues processed: 199 average time/residue: 0.1369 time to fit residues: 47.2747 Evaluate side-chains 195 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain B residue 1090 ASN Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 722 MET Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain C residue 1049 TYR Chi-restraints excluded: chain C residue 1107 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 417 MET Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 273 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 chunk 35 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 265 optimal weight: 7.9990 chunk 296 optimal weight: 0.9980 chunk 207 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.118063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.092142 restraints weight = 108174.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.091377 restraints weight = 75802.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.091296 restraints weight = 63210.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.091752 restraints weight = 65995.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.091822 restraints weight = 54355.429| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 26728 Z= 0.105 Angle : 0.593 15.042 36516 Z= 0.297 Chirality : 0.044 0.201 4302 Planarity : 0.004 0.065 4575 Dihedral : 4.584 27.184 3437 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.26 % Allowed : 13.93 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.24 (0.15), residues: 3161 helix: 1.22 (0.21), residues: 649 sheet: -0.47 (0.21), residues: 602 loop : -1.77 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1073 TYR 0.016 0.001 TYR C1049 PHE 0.083 0.001 PHE A 364 TRP 0.018 0.001 TRP C 423 HIS 0.003 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (26609) covalent geometry : angle 0.58349 / 0.30 (36204) SS BOND : bond 0.00261 / 0.16 ( 45) SS BOND : angle 0.81238 / 0.55 ( 90) hydrogen bonds : bond 0.03713 / 2.52 ( 900) hydrogen bonds : angle 5.23636 / 3.58 ( 2562) link_ALPHA1-3 : bond 0.00651 / 0.33 ( 5) link_ALPHA1-3 : angle 1.57808 / 1.13 ( 15) link_BETA1-4 : bond 0.00388 / 0.26 ( 35) link_BETA1-4 : angle 1.48594 / 1.06 ( 105) link_NAG-ASN : bond 0.00235 / 0.17 ( 34) link_NAG-ASN : angle 1.35658 / 0.93 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6322 Ramachandran restraints generated. 3161 Oldfield, 0 Emsley, 3161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.8299 (mmm) cc_final: 0.7927 (mmm) REVERT: B 81 ILE cc_start: 0.6663 (OUTLIER) cc_final: 0.6318 (mp) REVERT: B 87 ILE cc_start: 0.8672 (tt) cc_final: 0.8076 (mm) REVERT: B 107 MET cc_start: 0.4645 (mmt) cc_final: 0.4098 (mmt) REVERT: B 155 ASN cc_start: 0.8088 (m-40) cc_final: 0.7719 (m110) REVERT: B 231 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7145 (p90) REVERT: B 1099 THR cc_start: 0.8416 (p) cc_final: 0.8122 (t) REVERT: C 107 MET cc_start: 0.6119 (mmp) cc_final: 0.5855 (mmp) REVERT: C 262 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: C 407 ASP cc_start: 0.6469 (m-30) cc_final: 0.5329 (p0) REVERT: C 417 MET cc_start: 0.2540 (tpt) cc_final: -0.1599 (ptm) REVERT: C 758 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7993 (ttt180) REVERT: C 886 TYR cc_start: 0.7842 (t80) cc_final: 0.7601 (t80) REVERT: A 37 MET cc_start: 0.8107 (mtm) cc_final: 0.7657 (mpp) REVERT: A 151 MET cc_start: 0.5539 (mmm) cc_final: 0.3777 (tmm) REVERT: A 197 TYR cc_start: 0.8097 (m-10) cc_final: 0.7882 (m-10) REVERT: A 799 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8326 (t80) outliers start: 35 outliers final: 28 residues processed: 205 average time/residue: 0.1433 time to fit residues: 50.4274 Evaluate side-chains 195 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 207 ARG Chi-restraints excluded: chain B residue 231 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 909 PHE Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 733 ASN Chi-restraints excluded: chain A residue 799 PHE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 153 optimal weight: 8.9990 chunk 211 optimal weight: 0.0050 chunk 174 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 661 HIS ** C 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 227 ASN A 766 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.118036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.091884 restraints weight = 108007.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.090786 restraints weight = 75518.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.091060 restraints weight = 65370.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.091395 restraints weight = 61041.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.091583 restraints weight = 53376.774| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26728 Z= 0.108 Angle : 0.597 13.696 36516 Z= 0.300 Chirality : 0.044 0.195 4302 Planarity : 0.004 0.064 4575 Dihedral : 4.525 27.787 3437 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.33 % Allowed : 14.36 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -1.17 (0.15), residues: 3161 helix: 1.28 (0.21), residues: 650 sheet: -0.41 (0.21), residues: 606 loop : -1.73 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1073 TYR 0.016 0.001 TYR C1049 PHE 0.055 0.001 PHE A 364 TRP 0.016 0.001 TRP C 423 HIS 0.003 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (26609) covalent geometry : angle 0.58762 / 0.30 (36204) SS BOND : bond 0.00249 / 0.16 ( 45) SS BOND : angle 0.77923 / 0.52 ( 90) hydrogen bonds : bond 0.03707 / 2.51 ( 900) hydrogen bonds : angle 5.19342 / 3.55 ( 2562) link_ALPHA1-3 : bond 0.00650 / 0.33 ( 5) link_ALPHA1-3 : angle 1.56265 / 1.11 ( 15) link_BETA1-4 : bond 0.00367 / 0.25 ( 35) link_BETA1-4 : angle 1.48460 / 1.06 ( 105) link_NAG-ASN : bond 0.00215 / 0.15 ( 34) link_NAG-ASN : angle 1.33122 / 0.91 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.33 seconds wall clock time: 69 minutes 11.99 seconds (4151.99 seconds total)