Starting phenix.real_space_refine on Mon Jul 6 19:38:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xdl_33151/07_2026/7xdl_33151.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.053 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 162 5.16 5 C 24768 2.51 5 N 6427 2.21 5 O 7630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38987 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7863 Classifications: {'peptide': 1009} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 954} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7858 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 7858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7858 Classifications: {'peptide': 1008} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 54, 'TRANS': 953} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "E" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "G" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "H" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1609 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 13, 'TRANS': 197} Chain: "I" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1618 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "J" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "O" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain breaks: 1 Chain: "N" 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: 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: "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: 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: 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: 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: "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: 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 Time building chain proxies: 8.19, per 1000 atoms: 0.21 Number of scatterers: 38987 At special positions: 0 Unit cell: (182.82, 182.16, 242.22, 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 162 16.00 O 7630 8.00 N 6427 7.00 C 24768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 508 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 471 " distance=2.02 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 632 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.03 Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.03 Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 362 " - pdb=" SG CYS B 415 " distance=2.05 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 471 " distance=2.03 Simple disulfide: pdb=" SG CYS B 521 " - pdb=" SG CYS B 573 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 632 " distance=2.03 Simple disulfide: pdb=" SG CYS B 645 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.03 Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.03 Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 415 " distance=2.04 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 508 " distance=2.04 Simple disulfide: pdb=" SG CYS C 463 " - pdb=" SG CYS C 471 " distance=2.03 Simple disulfide: pdb=" SG CYS C 521 " - pdb=" SG CYS C 573 " distance=2.04 Simple disulfide: pdb=" SG CYS C 600 " - pdb=" SG CYS C 632 " distance=2.03 Simple disulfide: pdb=" SG CYS C 645 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.03 Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.03 Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 141 " - pdb=" SG CYS E 197 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS G 141 " - pdb=" SG CYS G 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 135 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 141 " - pdb=" SG CYS I 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 97 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1201 " - " ASN A1117 " " NAG A1202 " - " ASN A 692 " " NAG A1203 " - " ASN A1057 " " NAG A1204 " - " ASN A 640 " " NAG B1201 " - " ASN B1117 " " NAG B1202 " - " ASN B 692 " " NAG B1203 " - " ASN B1057 " " NAG B1204 " - " ASN B 640 " " NAG C1201 " - " ASN C1117 " " NAG C1202 " - " ASN C 692 " " NAG C1203 " - " ASN C1057 " " NAG C1204 " - " ASN C 640 " " NAG N 1 " - " ASN A1081 " " NAG Q 1 " - " ASN A 700 " " NAG R 1 " - " ASN A 784 " " NAG S 1 " - " ASN A 314 " " NAG T 1 " - " ASN B1081 " " NAG U 1 " - " ASN B 700 " " NAG V 1 " - " ASN B 784 " " NAG W 1 " - " ASN B 314 " " NAG X 1 " - " ASN C1081 " " NAG Y 1 " - " ASN C 700 " " NAG Z 1 " - " ASN C 784 " " NAG a 1 " - " ASN C 314 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9224 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 85 sheets defined 17.0% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.934A pdb=" N ASN A 371 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.891A pdb=" N ARG A 391 " --> pdb=" O ASP A 388 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 393 " --> pdb=" O VAL A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 599 through 606 removed outlier: 3.709A pdb=" N VAL A 603 " --> pdb=" O CYS A 600 " (cutoff:3.500A) Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 720 through 726 removed outlier: 3.550A pdb=" N TYR A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 737 removed outlier: 3.684A pdb=" N SER A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 743 through 766 removed outlier: 3.896A pdb=" N ASN A 747 " --> pdb=" O CYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 849 through 867 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 880 through 891 Processing helix chain 'A' and resid 895 through 902 removed outlier: 4.359A pdb=" N LEU A 899 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 removed outlier: 3.505A pdb=" N THR A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 950 removed outlier: 3.625A pdb=" N GLN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.639A pdb=" N ARG A 966 " --> pdb=" O ASP A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 1016 Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.640A pdb=" N TYR B 143 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER B 144 " --> pdb=" O GLY B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 144' Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.620A pdb=" N ASN B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.804A pdb=" N ARG B 391 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.611A pdb=" N ASN B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 726 Processing helix chain 'B' and resid 730 through 737 Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 744 through 766 Processing helix chain 'B' and resid 799 through 809 Processing helix chain 'B' and resid 849 through 867 Processing helix chain 'B' and resid 869 through 873 removed outlier: 3.541A pdb=" N GLY B 872 " --> pdb=" O TRP B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 880 through 891 Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.300A pdb=" N LEU B 899 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 924 Processing helix chain 'B' and resid 928 through 949 removed outlier: 3.608A pdb=" N GLN B 932 " --> pdb=" O LEU B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 959 through 966 removed outlier: 3.767A pdb=" N ILE B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 1015 Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 320 through 326 removed outlier: 4.276A pdb=" N VAL C 324 " --> pdb=" O PRO C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 353 Processing helix chain 'C' and resid 387 through 393 removed outlier: 4.021A pdb=" N ARG C 391 " --> pdb=" O ASP C 388 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 393 " --> pdb=" O VAL C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 720 through 726 Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 744 through 766 Processing helix chain 'C' and resid 799 through 809 removed outlier: 3.524A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 867 Processing helix chain 'C' and resid 869 through 873 Processing helix chain 'C' and resid 880 through 891 Processing helix chain 'C' and resid 896 through 901 Processing helix chain 'C' and resid 902 through 924 Processing helix chain 'C' and resid 928 through 950 removed outlier: 3.700A pdb=" N GLN C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER C 950 " --> pdb=" O VAL C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 966 removed outlier: 3.911A pdb=" N ILE C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 1016 Processing helix chain 'D' and resid 29 through 32 removed outlier: 3.536A pdb=" N SER D 32 " --> pdb=" O ILE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 32' Processing helix chain 'D' and resid 80 through 84 removed outlier: 3.804A pdb=" N PHE D 84 " --> pdb=" O PRO D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 183 through 190 removed outlier: 4.084A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.524A pdb=" N LYS E 64 " --> pdb=" O PRO E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.885A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 removed outlier: 3.785A pdb=" N GLY E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 159 No H-bonds generated for 'chain 'E' and resid 157 through 159' Processing helix chain 'F' and resid 29 through 32 removed outlier: 3.553A pdb=" N SER F 32 " --> pdb=" O ILE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 29 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.117A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 removed outlier: 3.706A pdb=" N LEU F 126 " --> pdb=" O SER F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.890A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 157 through 159 No H-bonds generated for 'chain 'G' and resid 157 through 159' Processing helix chain 'H' and resid 29 through 32 Processing helix chain 'H' and resid 122 through 129 removed outlier: 4.082A pdb=" N SER H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY H 129 " --> pdb=" O GLN H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.590A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 86 through 90 removed outlier: 3.960A pdb=" N THR I 90 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.810A pdb=" N THR I 132 " --> pdb=" O SER I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.568A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.623A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 15 removed outlier: 3.778A pdb=" N ALA A 12 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ASN A 46 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TYR A 252 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE A 184 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP A 211 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE A 186 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS A 190 " --> pdb=" O ALA A 205 " (cutoff:3.500A) removed outlier: 9.514A pdb=" N ALA A 205 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL A 21 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.654A pdb=" N GLY B 549 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ASP B 557 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.588A pdb=" N VAL A 32 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N THR A 257 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP A 273 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 259 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A 271 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS A 261 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.726A pdb=" N GLY A 88 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 91 " --> pdb=" O LEU A 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.786A pdb=" N PHE A 151 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 294 through 302 removed outlier: 6.780A pdb=" N VAL A 578 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASN A 300 " --> pdb=" O GLY A 576 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY A 576 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A 577 " --> pdb=" O GLN A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 311 removed outlier: 6.420A pdb=" N GLU A 307 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ASN A 525 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 309 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASP A 557 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY A 549 " --> pdb=" O ASP A 557 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE A 548 " --> pdb=" O PHE C 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 341 Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.657A pdb=" N CYS A 344 " --> pdb=" O CYS A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 436 through 437 Processing sheet with id=AB2, first strand: chain 'A' and resid 637 through 638 removed outlier: 6.532A pdb=" N ILE A 653 " --> pdb=" O ILE A 649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 685 removed outlier: 6.822A pdb=" N ALA A 684 " --> pdb=" O ILE C 771 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 694 through 711 removed outlier: 6.710A pdb=" N SER A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1059 " --> pdb=" O SER A 694 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 719 removed outlier: 4.521A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 842 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 770 through 772 removed outlier: 5.721A pdb=" N ILE A 771 " --> pdb=" O ASN B 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB8, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AB9, first strand: chain 'B' and resid 12 through 15 removed outlier: 4.084A pdb=" N ALA B 12 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN B 46 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR B 252 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 184 " --> pdb=" O ASP B 211 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP B 211 " --> pdb=" O PHE B 184 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 186 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU B 207 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N HIS B 190 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ALA B 205 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 21 " --> pdb=" O LEU B 206 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 28 removed outlier: 5.366A pdb=" N ASP C 557 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 529 " --> pdb=" O PHE C 526 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU C 307 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN C 523 " --> pdb=" O GLU C 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 40 removed outlier: 6.806A pdb=" N LYS B 261 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 69 through 70 removed outlier: 4.400A pdb=" N GLY B 88 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL B 115 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 294 through 302 removed outlier: 6.818A pdb=" N VAL B 578 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN B 300 " --> pdb=" O GLY B 576 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY B 576 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY B 577 " --> pdb=" O GLN B 596 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 337 through 341 Processing sheet with id=AC6, first strand: chain 'B' and resid 435 through 437 Processing sheet with id=AC7, first strand: chain 'B' and resid 637 through 643 removed outlier: 5.979A pdb=" N GLU B 637 " --> pdb=" O ALA B 677 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR B 679 " --> pdb=" O GLU B 637 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N VAL B 639 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA B 655 " --> pdb=" O PRO B 648 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 694 through 711 removed outlier: 6.847A pdb=" N SER B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B1059 " --> pdb=" O SER B 694 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 716 through 719 removed outlier: 4.704A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 771 through 772 removed outlier: 5.774A pdb=" N ILE B 771 " --> pdb=" O ASN C 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 1103 through 1108 removed outlier: 4.291A pdb=" N ALA B1070 " --> pdb=" O SER B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1077 through 1080 Processing sheet with id=AD4, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.801A pdb=" N ALA C 12 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ASN C 46 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N TYR C 252 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE C 184 " --> pdb=" O ASP C 211 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C 211 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE C 186 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N HIS C 190 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 9.077A pdb=" N ALA C 205 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N VAL C 21 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 40 removed outlier: 7.752A pdb=" N THR C 257 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 273 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU C 259 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA C 271 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS C 261 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.923A pdb=" N GLY C 88 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 294 through 302 removed outlier: 6.815A pdb=" N VAL C 578 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASN C 300 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 576 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY C 577 " --> pdb=" O GLN C 596 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.811A pdb=" N ASN C 337 " --> pdb=" O SER C 382 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 377 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 435 through 437 Processing sheet with id=AE1, first strand: chain 'C' and resid 637 through 643 removed outlier: 5.702A pdb=" N THR C 679 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN C 641 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE C 653 " --> pdb=" O ILE C 649 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 694 through 711 removed outlier: 6.672A pdb=" N SER C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C1059 " --> pdb=" O SER C 694 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY C1042 " --> pdb=" O SER C1038 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER C1038 " --> pdb=" O GLY C1042 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C1044 " --> pdb=" O PRO C1036 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU C1046 " --> pdb=" O SER C1034 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1034 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C1048 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 716 through 719 removed outlier: 4.603A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1103 through 1108 removed outlier: 4.405A pdb=" N ALA C1070 " --> pdb=" O SER C1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1077 through 1079 Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.571A pdb=" N LEU D 13 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.571A pdb=" N LEU D 13 " --> pdb=" O ASP D 106 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 98 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.536A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 145 through 151 Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AF3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.691A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.147A pdb=" N TYR E 177 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 121 through 124 removed outlier: 6.147A pdb=" N TYR E 177 " --> pdb=" O ASP E 145 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.644A pdb=" N TYR E 195 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.271A pdb=" N LEU F 11 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.271A pdb=" N LEU F 11 " --> pdb=" O ASP F 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR F 98 " --> pdb=" O GLN F 91 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 132 through 136 removed outlier: 3.654A pdb=" N VAL F 133 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 154 through 156 removed outlier: 4.710A pdb=" N TRP F 149 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL F 206 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 3 through 8 Processing sheet with id=AG4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.186A pdb=" N TRP G 34 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 40 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.812A pdb=" N LEU G 142 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR G 177 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.812A pdb=" N LEU G 142 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR G 177 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AG8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG9, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.029A pdb=" N LEU H 11 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR H 50 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.029A pdb=" N LEU H 11 " --> pdb=" O ASP H 106 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR H 98 " --> pdb=" O GLN H 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 118 through 119 removed outlier: 4.184A pdb=" N PHE H 119 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL H 134 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA H 131 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR H 179 " --> pdb=" O GLN H 161 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN H 161 " --> pdb=" O THR H 179 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 154 through 155 removed outlier: 4.219A pdb=" N TYR H 193 " --> pdb=" O PHE H 210 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE H 210 " --> pdb=" O TYR H 193 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AH5, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.620A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 121 through 123 removed outlier: 3.730A pdb=" N LEU I 142 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR I 177 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 151 through 155 Processing sheet with id=AH8, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AH9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.734A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 19 through 22 Processing sheet with id=AI2, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.192A pdb=" N CYS K 22 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA K 80 " --> pdb=" O CYS K 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.720A pdb=" N GLU K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.000A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE K 51 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE K 35 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP K 34 " --> pdb=" O HIS K 100 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.075A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI8, first strand: chain 'M' and resid 58 through 59 removed outlier: 4.601A pdb=" N TRP M 37 " --> pdb=" O MET M 49 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE M 51 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE M 35 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP M 34 " --> pdb=" O HIS M 100 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU M 110 " --> pdb=" O ARG M 99 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'O' and resid 5 through 6 removed outlier: 3.577A pdb=" N THR O 5 " --> pdb=" O ARG O 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE O 71 " --> pdb=" O CYS O 23 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AJ2, first strand: chain 'O' and resid 44 through 48 removed outlier: 6.540A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AJ4, first strand: chain 'P' and resid 58 through 59 removed outlier: 3.569A pdb=" N ASP P 58 " --> pdb=" O TYR P 53 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP P 48 " --> pdb=" O ARG P 39 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG P 39 " --> pdb=" O TRP P 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N GLY P 50 " --> pdb=" O TRP P 37 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP P 37 " --> pdb=" O GLY P 50 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TRP P 34 " --> pdb=" O HIS P 100 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR P 96 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU P 110 " --> pdb=" O ARG P 99 " (cutoff:3.500A) 1425 hydrogen bonds defined for protein. 3792 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: 10.73 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7113 1.33 - 1.46: 12894 1.46 - 1.59: 19688 1.59 - 1.72: 0 1.72 - 1.85: 207 Bond restraints: 39902 Sorted by residual: bond pdb=" N VAL B 324 " pdb=" CA VAL B 324 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N VAL F 133 " pdb=" CA VAL F 133 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N ILE F 118 " pdb=" CA ILE F 118 " ideal model delta sigma weight residual 1.456 1.498 -0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" CA SER C 574 " pdb=" CB SER C 574 " ideal model delta sigma weight residual 1.529 1.475 0.054 1.69e-02 3.50e+03 1.03e+01 bond pdb=" N SER H 183 " pdb=" CA SER H 183 " ideal model delta sigma weight residual 1.453 1.495 -0.042 1.31e-02 5.83e+03 1.03e+01 ... (remaining 39897 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 52218 1.85 - 3.71: 1768 3.71 - 5.56: 246 5.56 - 7.41: 43 7.41 - 9.26: 8 Bond angle restraints: 54283 Sorted by residual: angle pdb=" N PRO C 875 " pdb=" CA PRO C 875 " pdb=" CB PRO C 875 " ideal model delta sigma weight residual 103.36 110.30 -6.94 8.30e-01 1.45e+00 6.99e+01 angle pdb=" N PRO C 925 " pdb=" CA PRO C 925 " pdb=" CB PRO C 925 " ideal model delta sigma weight residual 101.88 110.04 -8.16 1.01e+00 9.80e-01 6.53e+01 angle pdb=" N PRO A 875 " pdb=" CA PRO A 875 " pdb=" CB PRO A 875 " ideal model delta sigma weight residual 103.34 110.30 -6.96 9.30e-01 1.16e+00 5.60e+01 angle pdb=" N PRO B 875 " pdb=" CA PRO B 875 " pdb=" CB PRO B 875 " ideal model delta sigma weight residual 103.19 110.24 -7.05 9.50e-01 1.11e+00 5.50e+01 angle pdb=" N PRO A 925 " pdb=" CA PRO A 925 " pdb=" CB PRO A 925 " ideal model delta sigma weight residual 102.76 110.12 -7.36 1.12e+00 7.97e-01 4.32e+01 ... (remaining 54278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 21341 17.98 - 35.95: 1697 35.95 - 53.93: 300 53.93 - 71.91: 55 71.91 - 89.88: 43 Dihedral angle restraints: 23436 sinusoidal: 9048 harmonic: 14388 Sorted by residual: dihedral pdb=" CB CYS C 274 " pdb=" SG CYS C 274 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual -86.00 -173.84 87.84 1 1.00e+01 1.00e-02 9.24e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 170.16 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 89 " pdb=" CB CYS F 89 " ideal model delta sinusoidal sigma weight residual 93.00 166.75 -73.75 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 23433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 6141 0.181 - 0.362: 58 0.362 - 0.543: 0 0.543 - 0.725: 1 0.725 - 0.906: 2 Chirality restraints: 6202 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1081 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.49 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C1081 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1081 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.21e+01 ... (remaining 6199 not shown) Planarity restraints: 6955 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR H 179 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.73e+00 pdb=" C THR H 179 " 0.054 2.00e-02 2.50e+03 pdb=" O THR H 179 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU H 180 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 190 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.63e+00 pdb=" C HIS H 190 " 0.045 2.00e-02 2.50e+03 pdb=" O HIS H 190 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS H 191 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 316 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C THR C 316 " -0.042 2.00e-02 2.50e+03 pdb=" O THR C 316 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN C 317 " 0.014 2.00e-02 2.50e+03 ... (remaining 6952 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2663 2.74 - 3.28: 36795 3.28 - 3.82: 60363 3.82 - 4.36: 73650 4.36 - 4.90: 130559 Nonbonded interactions: 304030 Sorted by model distance: nonbonded pdb=" NH1 ARG A 440 " pdb=" OD2 ASP A 450 " model vdw 2.195 3.120 nonbonded pdb=" OG SER E 154 " pdb=" OD1 ASN E 198 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 22 " pdb=" O LEU B 39 " model vdw 2.208 3.040 nonbonded pdb=" O ASN C 484 " pdb=" NE2 GLN C 489 " model vdw 2.210 3.120 nonbonded pdb=" OG SER H 122 " pdb=" OE1 GLU H 124 " model vdw 2.212 3.040 ... (remaining 304025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 605 or resid 623 through 1204)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'O' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.910 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: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 38.210 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.160 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.005 0.067 39995 Z= 0.292 Angle : 0.768 16.369 54505 Z= 0.460 Chirality : 0.056 0.906 6202 Planarity : 0.004 0.059 6931 Dihedral : 13.591 89.885 14041 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.07 % Favored : 94.85 % Rotamer: Outliers : 0.56 % Allowed : 1.04 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4894 helix: 1.97 (0.20), residues: 692 sheet: 0.41 (0.13), residues: 1583 loop : -1.21 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 966 TYR 0.031 0.001 TYR D 33 PHE 0.029 0.002 PHE B 889 TRP 0.032 0.002 TRP M 111 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.29 (39902) covalent geometry : angle 0.75048 / 0.46 (54283) SS BOND : bond 0.00503 / 0.36 ( 57) SS BOND : angle 1.50325 / 1.03 ( 114) hydrogen bonds : bond 0.14488 / 9.62 ( 1392) hydrogen bonds : angle 6.60857 / 4.51 ( 3792) link_BETA1-4 : bond 0.00368 / 0.26 ( 12) link_BETA1-4 : angle 1.86097 / 1.17 ( 36) link_NAG-ASN : bond 0.00533 / 0.30 ( 24) link_NAG-ASN : angle 4.10616 / 2.91 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 416 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 MET cc_start: 0.4213 (ptt) cc_final: 0.3835 (ttt) REVERT: D 18 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7253 (ttm-80) REVERT: K 20 ILE cc_start: 0.5021 (mt) cc_final: 0.4810 (mt) outliers start: 24 outliers final: 10 residues processed: 435 average time/residue: 0.2368 time to fit residues: 169.6781 Evaluate side-chains 350 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 340 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 185 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 432 optimal weight: 50.0000 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 0.0270 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 10.0000 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 ASN ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 ASN A 596 GLN A1084 HIS B 171 ASN B 405 ASN B 422 ASN B 489 GLN C 326 ASN C 405 ASN C 975 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 ASN H 125 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115453 restraints weight = 62745.435| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.14 r_work: 0.3174 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 39995 Z= 0.206 Angle : 0.653 17.540 54505 Z= 0.331 Chirality : 0.048 0.657 6202 Planarity : 0.005 0.056 6931 Dihedral : 5.057 59.761 5329 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.07 % Allowed : 8.03 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 4894 helix: 1.88 (0.20), residues: 707 sheet: 0.41 (0.13), residues: 1595 loop : -1.26 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 966 TYR 0.022 0.002 TYR D 33 PHE 0.028 0.002 PHE C 151 TRP 0.025 0.002 TRP I 155 HIS 0.011 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (39902) covalent geometry : angle 0.63103 / 0.33 (54283) SS BOND : bond 0.00481 / 0.35 ( 57) SS BOND : angle 1.44402 / 0.98 ( 114) hydrogen bonds : bond 0.05751 / 3.76 ( 1392) hydrogen bonds : angle 5.53394 / 3.76 ( 3792) link_BETA1-4 : bond 0.00490 / 0.30 ( 12) link_BETA1-4 : angle 1.08803 / 0.76 ( 36) link_NAG-ASN : bond 0.00480 / 0.32 ( 24) link_NAG-ASN : angle 4.28703 / 2.95 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 350 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 321 PHE cc_start: 0.7940 (p90) cc_final: 0.7636 (p90) REVERT: A 602 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: B 405 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8512 (m-40) REVERT: B 967 LEU cc_start: 0.7868 (mm) cc_final: 0.7663 (tp) REVERT: C 116 CYS cc_start: 0.4953 (OUTLIER) cc_final: 0.4523 (m) REVERT: C 138 MET cc_start: 0.4142 (ptt) cc_final: 0.3534 (ttt) REVERT: H 108 LYS cc_start: 0.7242 (ptmt) cc_final: 0.6937 (ttpt) REVERT: I 155 TRP cc_start: 0.5835 (m100) cc_final: 0.4896 (m100) REVERT: K 47 GLU cc_start: 0.7436 (mp0) cc_final: 0.7221 (mp0) REVERT: P 23 LYS cc_start: 0.7311 (tttp) cc_final: 0.6896 (tttp) REVERT: P 37 TRP cc_start: 0.6731 (m100) cc_final: 0.6497 (m100) REVERT: P 96 TYR cc_start: 0.4972 (m-10) cc_final: 0.4520 (m-80) outliers start: 46 outliers final: 33 residues processed: 382 average time/residue: 0.2459 time to fit residues: 155.1095 Evaluate side-chains 360 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 324 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 405 ASN Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 330 PHE Chi-restraints excluded: chain C residue 405 ASN Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 624 ASN Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 373 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 442 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 414 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 483 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 405 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 890 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 GLN ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.149312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101490 restraints weight = 63811.286| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.96 r_work: 0.3184 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 39995 Z= 0.262 Angle : 0.683 17.923 54505 Z= 0.346 Chirality : 0.049 0.636 6202 Planarity : 0.005 0.052 6931 Dihedral : 5.159 52.707 5327 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Rotamer: Outliers : 1.79 % Allowed : 10.86 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.12), residues: 4894 helix: 1.83 (0.20), residues: 700 sheet: 0.39 (0.13), residues: 1585 loop : -1.35 (0.11), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 966 TYR 0.024 0.002 TYR L 49 PHE 0.028 0.002 PHE C 321 TRP 0.017 0.002 TRP J 35 HIS 0.013 0.002 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.26 (39902) covalent geometry : angle 0.66094 / 0.34 (54283) SS BOND : bond 0.00530 / 0.36 ( 57) SS BOND : angle 1.57334 / 1.07 ( 114) hydrogen bonds : bond 0.06193 / 4.05 ( 1392) hydrogen bonds : angle 5.47254 / 3.71 ( 3792) link_BETA1-4 : bond 0.00277 / 0.17 ( 12) link_BETA1-4 : angle 1.17269 / 0.79 ( 36) link_NAG-ASN : bond 0.00517 / 0.32 ( 24) link_NAG-ASN : angle 4.36991 / 3.02 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 341 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 714 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8890 (ptp) REVERT: B 125 PHE cc_start: 0.6593 (p90) cc_final: 0.6333 (p90) REVERT: B 967 LEU cc_start: 0.7676 (mm) cc_final: 0.7412 (tp) REVERT: C 116 CYS cc_start: 0.5331 (OUTLIER) cc_final: 0.4787 (m) REVERT: C 125 PHE cc_start: 0.7765 (p90) cc_final: 0.7283 (p90) REVERT: C 138 MET cc_start: 0.3990 (ptt) cc_final: 0.3397 (ttt) REVERT: D 18 ARG cc_start: 0.8373 (mtp85) cc_final: 0.7709 (ttm-80) REVERT: H 108 LYS cc_start: 0.7564 (ptmt) cc_final: 0.7307 (ttpt) REVERT: I 155 TRP cc_start: 0.5771 (m100) cc_final: 0.4855 (m100) REVERT: K 49 MET cc_start: 0.5308 (pmm) cc_final: 0.4239 (ppp) REVERT: P 23 LYS cc_start: 0.7465 (tttp) cc_final: 0.7114 (tttp) REVERT: P 37 TRP cc_start: 0.6536 (m100) cc_final: 0.6300 (m100) REVERT: P 94 MET cc_start: 0.6150 (tmm) cc_final: 0.5586 (tmm) outliers start: 77 outliers final: 54 residues processed: 398 average time/residue: 0.2522 time to fit residues: 164.3493 Evaluate side-chains 382 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 326 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain P residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 266 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 437 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 226 optimal weight: 4.9990 chunk 178 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 179 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN F 125 GLN I 172 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN P 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.151380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.105527 restraints weight = 63383.748| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.00 r_work: 0.3211 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39995 Z= 0.143 Angle : 0.590 16.660 54505 Z= 0.297 Chirality : 0.046 0.593 6202 Planarity : 0.004 0.051 6931 Dihedral : 4.771 50.481 5323 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.48 % Rotamer: Outliers : 1.83 % Allowed : 12.91 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 4894 helix: 2.07 (0.20), residues: 695 sheet: 0.48 (0.13), residues: 1572 loop : -1.31 (0.11), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 966 TYR 0.036 0.001 TYR A 334 PHE 0.020 0.001 PHE C 151 TRP 0.014 0.001 TRP K 111 HIS 0.008 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (39902) covalent geometry : angle 0.56904 / 0.29 (54283) SS BOND : bond 0.00487 / 0.35 ( 57) SS BOND : angle 1.19339 / 0.82 ( 114) hydrogen bonds : bond 0.04901 / 3.18 ( 1392) hydrogen bonds : angle 5.15660 / 3.49 ( 3792) link_BETA1-4 : bond 0.00312 / 0.20 ( 12) link_BETA1-4 : angle 1.04302 / 0.69 ( 36) link_NAG-ASN : bond 0.00447 / 0.26 ( 24) link_NAG-ASN : angle 4.06909 / 2.81 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 363 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8298 (mm) REVERT: A 1074 ARG cc_start: 0.8524 (ttm170) cc_final: 0.8281 (ttm170) REVERT: B 125 PHE cc_start: 0.6623 (p90) cc_final: 0.6407 (p90) REVERT: B 388 ASP cc_start: 0.8820 (m-30) cc_final: 0.8572 (m-30) REVERT: B 791 ASP cc_start: 0.8124 (t0) cc_final: 0.7791 (t0) REVERT: C 116 CYS cc_start: 0.5209 (OUTLIER) cc_final: 0.4595 (m) REVERT: C 138 MET cc_start: 0.3987 (ptt) cc_final: 0.3368 (ttt) REVERT: H 61 ASP cc_start: 0.7752 (m-30) cc_final: 0.7516 (t0) REVERT: H 108 LYS cc_start: 0.7537 (ptmt) cc_final: 0.7301 (ttpt) REVERT: I 155 TRP cc_start: 0.5667 (m100) cc_final: 0.4845 (m100) REVERT: K 49 MET cc_start: 0.5132 (OUTLIER) cc_final: 0.4216 (ppp) REVERT: M 46 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6308 (mp) REVERT: P 23 LYS cc_start: 0.7449 (tttp) cc_final: 0.7135 (tttp) REVERT: P 94 MET cc_start: 0.6219 (tmm) cc_final: 0.5521 (tmm) outliers start: 79 outliers final: 46 residues processed: 425 average time/residue: 0.2258 time to fit residues: 158.1168 Evaluate side-chains 390 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 59 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 235 optimal weight: 4.9990 chunk 356 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 280 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 361 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 321 optimal weight: 0.8980 chunk 343 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN O 37 GLN O 90 GLN P 66 GLN P 100 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.151060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105055 restraints weight = 63333.168| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 3.05 r_work: 0.3216 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 39995 Z= 0.150 Angle : 0.594 16.395 54505 Z= 0.299 Chirality : 0.046 0.574 6202 Planarity : 0.004 0.051 6931 Dihedral : 4.688 51.115 5322 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.09 % Allowed : 14.00 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4894 helix: 2.13 (0.20), residues: 697 sheet: 0.51 (0.13), residues: 1559 loop : -1.25 (0.11), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 966 TYR 0.027 0.001 TYR A 334 PHE 0.024 0.001 PHE C 151 TRP 0.011 0.001 TRP P 37 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (39902) covalent geometry : angle 0.57266 / 0.29 (54283) SS BOND : bond 0.00493 / 0.32 ( 57) SS BOND : angle 1.40202 / 0.86 ( 114) hydrogen bonds : bond 0.04945 / 3.22 ( 1392) hydrogen bonds : angle 5.12100 / 3.47 ( 3792) link_BETA1-4 : bond 0.00311 / 0.20 ( 12) link_BETA1-4 : angle 1.07266 / 0.71 ( 36) link_NAG-ASN : bond 0.00452 / 0.26 ( 24) link_NAG-ASN : angle 3.99277 / 2.76 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 354 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 116 CYS cc_start: 0.5633 (OUTLIER) cc_final: 0.5223 (m) REVERT: A 143 TYR cc_start: 0.4691 (OUTLIER) cc_final: 0.2526 (m-80) REVERT: A 1075 GLU cc_start: 0.8385 (tt0) cc_final: 0.8123 (pp20) REVERT: B 125 PHE cc_start: 0.6728 (p90) cc_final: 0.6475 (p90) REVERT: B 791 ASP cc_start: 0.8049 (t0) cc_final: 0.7718 (t0) REVERT: B 967 LEU cc_start: 0.7558 (tp) cc_final: 0.7332 (tp) REVERT: C 138 MET cc_start: 0.3957 (ptt) cc_final: 0.3367 (ttt) REVERT: D 184 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7506 (mmmm) REVERT: H 108 LYS cc_start: 0.7555 (ptmt) cc_final: 0.7311 (ttpt) REVERT: H 176 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6941 (tp) REVERT: H 180 LEU cc_start: 0.5552 (mt) cc_final: 0.5346 (mt) REVERT: I 155 TRP cc_start: 0.5655 (m100) cc_final: 0.4988 (m100) REVERT: K 40 GLN cc_start: 0.6994 (tm130) cc_final: 0.6062 (tm-30) REVERT: K 49 MET cc_start: 0.5140 (OUTLIER) cc_final: 0.4208 (ppp) REVERT: O 37 GLN cc_start: 0.6473 (tp-100) cc_final: 0.6115 (tp-100) REVERT: O 39 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6244 (ttpt) REVERT: P 3 GLN cc_start: 0.6093 (pm20) cc_final: 0.5856 (pm20) REVERT: P 23 LYS cc_start: 0.7406 (tttp) cc_final: 0.7124 (tttp) REVERT: P 37 TRP cc_start: 0.6396 (m100) cc_final: 0.6121 (m-90) REVERT: P 94 MET cc_start: 0.6241 (tmm) cc_final: 0.5405 (tmm) outliers start: 90 outliers final: 68 residues processed: 423 average time/residue: 0.2405 time to fit residues: 168.5352 Evaluate side-chains 414 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 340 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 350 optimal weight: 0.9990 chunk 198 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 438 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 384 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 ASN A1089 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN C 300 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 66 GLN O 90 GLN P 100 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.148933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103380 restraints weight = 63407.269| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.08 r_work: 0.3181 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 39995 Z= 0.225 Angle : 0.658 16.702 54505 Z= 0.331 Chirality : 0.048 0.582 6202 Planarity : 0.004 0.054 6931 Dihedral : 4.940 51.813 5321 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.41 % Favored : 94.54 % Rotamer: Outliers : 2.95 % Allowed : 14.21 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 4894 helix: 1.94 (0.20), residues: 698 sheet: 0.45 (0.13), residues: 1564 loop : -1.29 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 966 TYR 0.027 0.002 TYR L 49 PHE 0.030 0.002 PHE C 321 TRP 0.013 0.002 TRP P 84 HIS 0.012 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.22 (39902) covalent geometry : angle 0.63678 / 0.33 (54283) SS BOND : bond 0.00592 / 0.38 ( 57) SS BOND : angle 1.71426 / 1.07 ( 114) hydrogen bonds : bond 0.05845 / 3.82 ( 1392) hydrogen bonds : angle 5.25708 / 3.56 ( 3792) link_BETA1-4 : bond 0.00284 / 0.19 ( 12) link_BETA1-4 : angle 1.17868 / 0.79 ( 36) link_NAG-ASN : bond 0.00493 / 0.30 ( 24) link_NAG-ASN : angle 4.09751 / 2.84 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 349 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 116 CYS cc_start: 0.5779 (OUTLIER) cc_final: 0.5354 (m) REVERT: A 143 TYR cc_start: 0.4946 (OUTLIER) cc_final: 0.2650 (m-80) REVERT: A 1094 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8447 (pp20) REVERT: B 125 PHE cc_start: 0.6774 (p90) cc_final: 0.6481 (p90) REVERT: B 791 ASP cc_start: 0.8096 (t0) cc_final: 0.7699 (t0) REVERT: B 967 LEU cc_start: 0.7619 (tp) cc_final: 0.7404 (tp) REVERT: C 138 MET cc_start: 0.3798 (ptt) cc_final: 0.3416 (ttt) REVERT: C 1125 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7896 (mm110) REVERT: D 90 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: D 124 GLU cc_start: 0.7909 (tt0) cc_final: 0.7649 (tt0) REVERT: D 184 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7486 (mmmm) REVERT: H 108 LYS cc_start: 0.7596 (ptmt) cc_final: 0.7358 (ttpt) REVERT: I 155 TRP cc_start: 0.5696 (m100) cc_final: 0.5216 (m100) REVERT: K 49 MET cc_start: 0.5177 (OUTLIER) cc_final: 0.4249 (ppp) REVERT: M 94 MET cc_start: 0.6471 (tpt) cc_final: 0.5736 (tpt) REVERT: P 3 GLN cc_start: 0.6154 (pm20) cc_final: 0.5905 (pm20) REVERT: P 37 TRP cc_start: 0.6392 (m100) cc_final: 0.6152 (m-90) REVERT: P 94 MET cc_start: 0.6248 (tmm) cc_final: 0.5699 (tmm) outliers start: 127 outliers final: 92 residues processed: 454 average time/residue: 0.2351 time to fit residues: 176.5958 Evaluate side-chains 443 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 344 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 51 HIS Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 300 ASN Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 659 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 246 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 356 optimal weight: 6.9990 chunk 416 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 288 optimal weight: 0.9990 chunk 308 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 171 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.112786 restraints weight = 63426.595| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.48 r_work: 0.3217 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 39995 Z= 0.128 Angle : 0.583 15.794 54505 Z= 0.293 Chirality : 0.045 0.560 6202 Planarity : 0.004 0.053 6931 Dihedral : 4.663 52.412 5321 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.37 % Favored : 95.59 % Rotamer: Outliers : 2.51 % Allowed : 15.16 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 4894 helix: 2.17 (0.20), residues: 695 sheet: 0.54 (0.13), residues: 1554 loop : -1.25 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 966 TYR 0.036 0.001 TYR A 334 PHE 0.021 0.001 PHE B 77 TRP 0.012 0.001 TRP I 47 HIS 0.007 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (39902) covalent geometry : angle 0.56341 / 0.29 (54283) SS BOND : bond 0.00532 / 0.32 ( 57) SS BOND : angle 1.26949 / 0.77 ( 114) hydrogen bonds : bond 0.04663 / 3.02 ( 1392) hydrogen bonds : angle 5.03400 / 3.42 ( 3792) link_BETA1-4 : bond 0.00322 / 0.21 ( 12) link_BETA1-4 : angle 1.06641 / 0.69 ( 36) link_NAG-ASN : bond 0.00445 / 0.26 ( 24) link_NAG-ASN : angle 3.86123 / 2.67 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 354 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5282 (m) REVERT: A 143 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.2343 (m-80) REVERT: A 1094 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8419 (pp20) REVERT: B 125 PHE cc_start: 0.6770 (p90) cc_final: 0.6492 (p90) REVERT: B 791 ASP cc_start: 0.8024 (t0) cc_final: 0.7709 (t0) REVERT: C 138 MET cc_start: 0.3737 (ptt) cc_final: 0.3373 (ttt) REVERT: C 1125 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7888 (mm110) REVERT: D 71 ASP cc_start: 0.8444 (t0) cc_final: 0.8229 (m-30) REVERT: D 184 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7569 (mmmm) REVERT: H 108 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7278 (ttpt) REVERT: H 109 ARG cc_start: 0.4021 (OUTLIER) cc_final: 0.3329 (pmt-80) REVERT: H 176 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7081 (tp) REVERT: I 155 TRP cc_start: 0.5693 (m100) cc_final: 0.5323 (m100) REVERT: K 49 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4296 (ppp) REVERT: P 37 TRP cc_start: 0.6343 (m100) cc_final: 0.6005 (m-90) REVERT: P 94 MET cc_start: 0.6193 (tmm) cc_final: 0.5634 (tmm) REVERT: P 111 TRP cc_start: 0.7228 (OUTLIER) cc_final: 0.5225 (m-10) outliers start: 108 outliers final: 81 residues processed: 443 average time/residue: 0.2386 time to fit residues: 174.2535 Evaluate side-chains 428 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 339 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 869 TRP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 735 LEU Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 297 optimal weight: 5.9990 chunk 431 optimal weight: 7.9990 chunk 253 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 326 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 467 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 365 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN P 100 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.153068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107780 restraints weight = 63412.727| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.92 r_work: 0.3260 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 39995 Z= 0.109 Angle : 0.563 15.204 54505 Z= 0.283 Chirality : 0.045 0.532 6202 Planarity : 0.004 0.053 6931 Dihedral : 4.489 52.671 5321 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.65 % Rotamer: Outliers : 2.51 % Allowed : 15.11 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.12), residues: 4894 helix: 2.30 (0.20), residues: 695 sheet: 0.59 (0.13), residues: 1555 loop : -1.17 (0.11), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 966 TYR 0.032 0.001 TYR A 334 PHE 0.022 0.001 PHE B 77 TRP 0.010 0.001 TRP J 35 HIS 0.006 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (39902) covalent geometry : angle 0.54353 / 0.28 (54283) SS BOND : bond 0.00465 / 0.29 ( 57) SS BOND : angle 1.36490 / 0.90 ( 114) hydrogen bonds : bond 0.04210 / 2.72 ( 1392) hydrogen bonds : angle 4.90007 / 3.33 ( 3792) link_BETA1-4 : bond 0.00313 / 0.20 ( 12) link_BETA1-4 : angle 1.03599 / 0.68 ( 36) link_NAG-ASN : bond 0.00461 / 0.27 ( 24) link_NAG-ASN : angle 3.69274 / 2.56 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 358 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5605 (OUTLIER) cc_final: 0.5204 (m) REVERT: A 143 TYR cc_start: 0.4847 (OUTLIER) cc_final: 0.2237 (m-80) REVERT: A 602 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8020 (pt0) REVERT: A 1074 ARG cc_start: 0.8582 (ttm170) cc_final: 0.8336 (ttm170) REVERT: A 1094 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (pp20) REVERT: B 125 PHE cc_start: 0.6779 (p90) cc_final: 0.6521 (p90) REVERT: B 791 ASP cc_start: 0.7942 (t0) cc_final: 0.7621 (t0) REVERT: B 1033 MET cc_start: 0.8972 (ptm) cc_final: 0.8763 (ptm) REVERT: C 138 MET cc_start: 0.3758 (ptt) cc_final: 0.3379 (ttt) REVERT: C 488 TYR cc_start: 0.6821 (t80) cc_final: 0.6541 (t80) REVERT: C 1125 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7916 (mm110) REVERT: D 71 ASP cc_start: 0.8378 (t0) cc_final: 0.8163 (m-30) REVERT: D 184 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7506 (mmmm) REVERT: H 108 LYS cc_start: 0.7572 (ptmt) cc_final: 0.7283 (ttpt) REVERT: H 109 ARG cc_start: 0.4041 (OUTLIER) cc_final: 0.3460 (pmt-80) REVERT: H 176 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6644 (mp) REVERT: I 38 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8147 (ptp-170) REVERT: I 155 TRP cc_start: 0.5544 (m100) cc_final: 0.5171 (m100) REVERT: K 49 MET cc_start: 0.5182 (OUTLIER) cc_final: 0.3773 (ppp) REVERT: O 39 LYS cc_start: 0.7495 (mmmt) cc_final: 0.6468 (tmmt) REVERT: P 3 GLN cc_start: 0.6156 (pm20) cc_final: 0.5937 (pm20) REVERT: P 37 TRP cc_start: 0.6259 (m100) cc_final: 0.5930 (m-90) REVERT: P 94 MET cc_start: 0.6184 (tmm) cc_final: 0.5562 (tmm) REVERT: P 111 TRP cc_start: 0.7204 (OUTLIER) cc_final: 0.5383 (m-10) outliers start: 108 outliers final: 82 residues processed: 444 average time/residue: 0.2355 time to fit residues: 172.7784 Evaluate side-chains 440 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 348 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 869 TRP Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1075 GLU Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 132 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 150 optimal weight: 0.0070 chunk 123 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 464 optimal weight: 20.0000 chunk 316 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 338 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 58 ASN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.150817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.105663 restraints weight = 63326.218| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.16 r_work: 0.3209 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39995 Z= 0.166 Angle : 0.606 15.475 54505 Z= 0.304 Chirality : 0.046 0.531 6202 Planarity : 0.004 0.055 6931 Dihedral : 4.635 53.101 5321 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Rotamer: Outliers : 2.55 % Allowed : 15.27 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4894 helix: 2.20 (0.20), residues: 696 sheet: 0.55 (0.13), residues: 1564 loop : -1.20 (0.11), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 966 TYR 0.029 0.001 TYR A 334 PHE 0.020 0.001 PHE C 321 TRP 0.011 0.001 TRP P 84 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (39902) covalent geometry : angle 0.58655 / 0.30 (54283) SS BOND : bond 0.00513 / 0.34 ( 57) SS BOND : angle 1.65300 / 1.17 ( 114) hydrogen bonds : bond 0.05008 / 3.26 ( 1392) hydrogen bonds : angle 5.00648 / 3.40 ( 3792) link_BETA1-4 : bond 0.00289 / 0.19 ( 12) link_BETA1-4 : angle 1.09651 / 0.73 ( 36) link_NAG-ASN : bond 0.00461 / 0.27 ( 24) link_NAG-ASN : angle 3.75108 / 2.61 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 338 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A 116 CYS cc_start: 0.5673 (OUTLIER) cc_final: 0.5234 (m) REVERT: A 143 TYR cc_start: 0.4791 (OUTLIER) cc_final: 0.2342 (m-80) REVERT: A 1094 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8342 (pp20) REVERT: B 125 PHE cc_start: 0.6773 (p90) cc_final: 0.6490 (p90) REVERT: B 791 ASP cc_start: 0.8034 (t0) cc_final: 0.7663 (t0) REVERT: C 138 MET cc_start: 0.3606 (ptt) cc_final: 0.3333 (ttt) REVERT: C 1125 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7975 (mm110) REVERT: D 18 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7736 (ttm-80) REVERT: D 71 ASP cc_start: 0.8413 (t0) cc_final: 0.8195 (m-30) REVERT: D 124 GLU cc_start: 0.7835 (tt0) cc_final: 0.7590 (tt0) REVERT: D 184 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7464 (mmmm) REVERT: H 108 LYS cc_start: 0.7603 (ptmt) cc_final: 0.7306 (ttpt) REVERT: H 109 ARG cc_start: 0.4071 (OUTLIER) cc_final: 0.3318 (pmt-80) REVERT: H 176 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7108 (tp) REVERT: I 38 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8179 (ptp-170) REVERT: I 69 MET cc_start: 0.9000 (mtt) cc_final: 0.8753 (mtt) REVERT: I 155 TRP cc_start: 0.5530 (m100) cc_final: 0.5065 (m100) REVERT: K 49 MET cc_start: 0.5270 (OUTLIER) cc_final: 0.4313 (ppp) REVERT: O 39 LYS cc_start: 0.7514 (mmmt) cc_final: 0.6474 (tmmt) REVERT: P 3 GLN cc_start: 0.6189 (pm20) cc_final: 0.5980 (pm20) REVERT: P 37 TRP cc_start: 0.6235 (m100) cc_final: 0.5942 (m-90) REVERT: P 94 MET cc_start: 0.6193 (tmm) cc_final: 0.5484 (tmm) REVERT: P 111 TRP cc_start: 0.7192 (OUTLIER) cc_final: 0.5182 (m-10) outliers start: 110 outliers final: 90 residues processed: 429 average time/residue: 0.2315 time to fit residues: 165.0674 Evaluate side-chains 436 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 336 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 143 TYR Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 712 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 431 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 251 optimal weight: 7.9990 chunk 442 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 462 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 300 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 ASN E 201 HIS J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN P 100 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.147233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098834 restraints weight = 63430.532| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.03 r_work: 0.3130 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 39995 Z= 0.327 Angle : 0.748 16.851 54505 Z= 0.379 Chirality : 0.052 0.567 6202 Planarity : 0.005 0.059 6931 Dihedral : 5.247 53.387 5321 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.25 % Favored : 93.71 % Rotamer: Outliers : 2.58 % Allowed : 15.37 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4894 helix: 1.68 (0.20), residues: 699 sheet: 0.35 (0.13), residues: 1581 loop : -1.37 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 966 TYR 0.026 0.002 TYR A 334 PHE 0.036 0.002 PHE C 321 TRP 0.023 0.002 TRP M 84 HIS 0.014 0.002 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00810 / 0.33 (39902) covalent geometry : angle 0.72653 / 0.37 (54283) SS BOND : bond 0.00686 / 0.45 ( 57) SS BOND : angle 2.16155 / 1.50 ( 114) hydrogen bonds : bond 0.06758 / 4.42 ( 1392) hydrogen bonds : angle 5.44865 / 3.69 ( 3792) link_BETA1-4 : bond 0.00276 / 0.18 ( 12) link_BETA1-4 : angle 1.36329 / 0.91 ( 36) link_NAG-ASN : bond 0.00553 / 0.35 ( 24) link_NAG-ASN : angle 4.15887 / 2.90 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9788 Ramachandran restraints generated. 4894 Oldfield, 0 Emsley, 4894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 336 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8371 (mm) REVERT: A 116 CYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5479 (m) REVERT: A 1094 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8489 (pp20) REVERT: B 125 PHE cc_start: 0.6796 (p90) cc_final: 0.6456 (p90) REVERT: B 388 ASP cc_start: 0.8879 (m-30) cc_final: 0.8644 (m-30) REVERT: B 791 ASP cc_start: 0.8237 (t0) cc_final: 0.7837 (t0) REVERT: C 138 MET cc_start: 0.3684 (ptt) cc_final: 0.3427 (ttt) REVERT: C 1125 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7955 (mm110) REVERT: D 184 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7592 (mmmm) REVERT: F 24 ARG cc_start: 0.7281 (mtp85) cc_final: 0.7049 (ttm-80) REVERT: H 108 LYS cc_start: 0.7665 (ptmt) cc_final: 0.7339 (ttpt) REVERT: I 38 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8048 (ptp-170) REVERT: I 155 TRP cc_start: 0.5884 (m100) cc_final: 0.5403 (m100) REVERT: K 49 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.4324 (ppp) REVERT: M 40 GLN cc_start: 0.7309 (tp-100) cc_final: 0.7029 (tp-100) REVERT: P 3 GLN cc_start: 0.6184 (pm20) cc_final: 0.5970 (pm20) REVERT: P 37 TRP cc_start: 0.6293 (m100) cc_final: 0.6069 (m-90) REVERT: P 94 MET cc_start: 0.6337 (tmm) cc_final: 0.5435 (tmm) REVERT: P 111 TRP cc_start: 0.7200 (OUTLIER) cc_final: 0.5190 (m-10) outliers start: 111 outliers final: 91 residues processed: 430 average time/residue: 0.2296 time to fit residues: 162.5371 Evaluate side-chains 426 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 328 time to evaluate : 1.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 116 CYS Chi-restraints excluded: chain A residue 120 PHE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 688 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 742 PHE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1101 ASP Chi-restraints excluded: chain A residue 1116 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 319 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 803 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 917 ILE Chi-restraints excluded: chain B residue 959 VAL Chi-restraints excluded: chain B residue 1064 ILE Chi-restraints excluded: chain B residue 1116 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 116 CYS Chi-restraints excluded: chain C residue 120 PHE Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 221 PHE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 946 VAL Chi-restraints excluded: chain C residue 1064 ILE Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 118 ILE Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 38 ARG Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 49 MET Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 111 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 442 optimal weight: 0.0040 chunk 191 optimal weight: 2.9990 chunk 25 optimal weight: 0.0040 chunk 487 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 356 optimal weight: 2.9990 chunk 321 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 392 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 overall best weight: 0.6406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 171 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN E 5 GLN E 50 GLN E 58 ASN ** E 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 GLN I 77 GLN J 90 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.114559 restraints weight = 63368.599| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.38 r_work: 0.3252 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 39995 Z= 0.109 Angle : 0.587 15.081 54505 Z= 0.296 Chirality : 0.045 0.540 6202 Planarity : 0.004 0.054 6931 Dihedral : 4.672 54.029 5320 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 1.90 % Allowed : 16.39 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4894 helix: 2.13 (0.20), residues: 694 sheet: 0.53 (0.13), residues: 1569 loop : -1.22 (0.11), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 18 TYR 0.026 0.001 TYR L 49 PHE 0.023 0.001 PHE B 77 TRP 0.014 0.001 TRP E 47 HIS 0.007 0.001 HIS I 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (39902) covalent geometry : angle 0.56884 / 0.29 (54283) SS BOND : bond 0.00462 / 0.32 ( 57) SS BOND : angle 1.28141 / 0.88 ( 114) hydrogen bonds : bond 0.04300 / 2.77 ( 1392) hydrogen bonds : angle 5.02299 / 3.42 ( 3792) link_BETA1-4 : bond 0.00383 / 0.25 ( 12) link_BETA1-4 : angle 1.06822 / 0.67 ( 36) link_NAG-ASN : bond 0.00465 / 0.28 ( 24) link_NAG-ASN : angle 3.67538 / 2.54 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16545.71 seconds wall clock time: 281 minutes 51.43 seconds (16911.43 seconds total)