Starting phenix.real_space_refine on Sat Mar 7 05:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xdl_33151/03_2026/7xdl_33151.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xdl_33151/03_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_33151/03_2026/7xdl_33151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xdl_33151/03_2026/7xdl_33151.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xdl_33151/03_2026/7xdl_33151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xdl_33151/03_2026/7xdl_33151.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.80, per 1000 atoms: 0.23 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: 3.07 Conformation dependent library (CDL) restraints added in 1.8 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: 1.85 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: 11.81 Time building geometry restraints manager: 4.10 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: 22013 17.98 - 35.95: 1749 35.95 - 53.93: 330 53.93 - 71.91: 57 71.91 - 89.88: 43 Dihedral angle restraints: 24192 sinusoidal: 9804 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 24189 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: 11.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.060 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 38.760 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 13.527 89.885 14797 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 covalent geometry : bond 0.00503 (39902) covalent geometry : angle 0.75048 (54283) SS BOND : bond 0.00503 ( 57) SS BOND : angle 1.50325 ( 114) hydrogen bonds : bond 0.14488 ( 1392) hydrogen bonds : angle 6.60857 ( 3792) link_BETA1-4 : bond 0.00368 ( 12) link_BETA1-4 : angle 1.86097 ( 36) link_NAG-ASN : bond 0.00533 ( 24) link_NAG-ASN : angle 4.10616 ( 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 : 1.367 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: 0.2261 time to fit residues: 162.8790 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 : 1.433 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.146210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116272 restraints weight = 62744.451| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.12 r_work: 0.3189 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 39995 Z= 0.205 Angle : 0.651 17.656 54505 Z= 0.330 Chirality : 0.049 0.743 6202 Planarity : 0.005 0.055 6931 Dihedral : 5.955 59.749 6085 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 1.04 % Allowed : 8.01 % Favored : 90.95 % 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: 1.89 (0.20), residues: 707 sheet: 0.41 (0.13), residues: 1593 loop : -1.25 (0.11), residues: 2594 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 0.029 0.002 PHE C 151 TRP 0.021 0.002 TRP I 155 HIS 0.011 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00503 (39902) covalent geometry : angle 0.62909 (54283) SS BOND : bond 0.00508 ( 57) SS BOND : angle 1.43640 ( 114) hydrogen bonds : bond 0.05779 ( 1392) hydrogen bonds : angle 5.53817 ( 3792) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 1.17790 ( 36) link_NAG-ASN : bond 0.00529 ( 24) link_NAG-ASN : angle 4.35385 ( 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 394 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 349 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: A 321 PHE cc_start: 0.7936 (p90) cc_final: 0.7630 (p90) REVERT: A 602 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 405 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8503 (m-40) REVERT: B 967 LEU cc_start: 0.7865 (mm) cc_final: 0.7665 (tp) REVERT: C 116 CYS cc_start: 0.4891 (OUTLIER) cc_final: 0.4458 (m) REVERT: C 138 MET cc_start: 0.4159 (ptt) cc_final: 0.3567 (ttt) REVERT: H 108 LYS cc_start: 0.7213 (ptmt) cc_final: 0.6907 (ttpt) REVERT: I 155 TRP cc_start: 0.5862 (m100) cc_final: 0.4888 (m100) REVERT: P 23 LYS cc_start: 0.7276 (tttp) cc_final: 0.6851 (tttp) REVERT: P 37 TRP cc_start: 0.6722 (m100) cc_final: 0.6487 (m100) REVERT: P 96 TYR cc_start: 0.4970 (m-10) cc_final: 0.4522 (m-80) outliers start: 45 outliers final: 33 residues processed: 381 average time/residue: 0.2277 time to fit residues: 143.6133 Evaluate side-chains 359 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 323 time to evaluate : 1.355 ------------------------------------------------------------------------------- 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: 7.9990 chunk 442 optimal weight: 0.6980 chunk 390 optimal weight: 9.9990 chunk 414 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 483 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3937 r_free = 0.3937 target = 0.145473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.115230 restraints weight = 62774.927| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.19 r_work: 0.3161 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1111 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= 0.209 Angle : 0.641 17.794 54505 Z= 0.324 Chirality : 0.048 0.677 6202 Planarity : 0.004 0.051 6931 Dihedral : 5.789 55.541 6083 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 1.56 % Allowed : 10.89 % Favored : 87.56 % 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: 1.97 (0.20), residues: 698 sheet: 0.44 (0.13), residues: 1584 loop : -1.30 (0.11), residues: 2612 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 0.024 0.002 PHE B 889 TRP 0.016 0.002 TRP J 35 HIS 0.011 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00513 (39902) covalent geometry : angle 0.61851 (54283) SS BOND : bond 0.00476 ( 57) SS BOND : angle 1.40025 ( 114) hydrogen bonds : bond 0.05692 ( 1392) hydrogen bonds : angle 5.37208 ( 3792) link_BETA1-4 : bond 0.00281 ( 12) link_BETA1-4 : angle 1.26537 ( 36) link_NAG-ASN : bond 0.00502 ( 24) link_NAG-ASN : angle 4.34477 ( 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 414 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 347 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 116 CYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4541 (m) REVERT: C 125 PHE cc_start: 0.7584 (p90) cc_final: 0.7204 (p90) REVERT: C 138 MET cc_start: 0.4213 (ptt) cc_final: 0.3597 (ttt) REVERT: I 155 TRP cc_start: 0.6064 (m100) cc_final: 0.5225 (m100) REVERT: K 49 MET cc_start: 0.5108 (pmm) cc_final: 0.4315 (ppp) REVERT: M 94 MET cc_start: 0.7128 (tpp) cc_final: 0.6896 (tpt) REVERT: P 23 LYS cc_start: 0.7302 (tttp) cc_final: 0.6874 (tttp) REVERT: P 94 MET cc_start: 0.6432 (tmm) cc_final: 0.5809 (tmm) outliers start: 67 outliers final: 49 residues processed: 396 average time/residue: 0.2297 time to fit residues: 150.0877 Evaluate side-chains 381 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 331 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 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 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 341 ILE 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 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 769 LYS Chi-restraints excluded: chain C residue 917 ILE 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 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: 0.6980 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 437 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 226 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 = 0.4037 r_free = 0.4037 target = 0.150428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.103018 restraints weight = 63367.286| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.03 r_work: 0.3199 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 39995 Z= 0.185 Angle : 0.619 17.264 54505 Z= 0.312 Chirality : 0.047 0.663 6202 Planarity : 0.004 0.051 6931 Dihedral : 5.580 54.443 6079 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.99 % Favored : 94.97 % Rotamer: Outliers : 2.18 % Allowed : 12.28 % Favored : 85.54 % 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: 2.01 (0.20), residues: 697 sheet: 0.47 (0.13), residues: 1578 loop : -1.31 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 966 TYR 0.025 0.002 TYR L 49 PHE 0.024 0.002 PHE C 151 TRP 0.013 0.001 TRP K 111 HIS 0.009 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00452 (39902) covalent geometry : angle 0.59630 (54283) SS BOND : bond 0.00482 ( 57) SS BOND : angle 1.32987 ( 114) hydrogen bonds : bond 0.05385 ( 1392) hydrogen bonds : angle 5.26338 ( 3792) link_BETA1-4 : bond 0.00252 ( 12) link_BETA1-4 : angle 1.27435 ( 36) link_NAG-ASN : bond 0.00463 ( 24) link_NAG-ASN : angle 4.26162 ( 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 450 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 356 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8324 (mm) REVERT: B 388 ASP cc_start: 0.8854 (m-30) cc_final: 0.8623 (m-30) REVERT: C 116 CYS cc_start: 0.5207 (OUTLIER) cc_final: 0.4616 (m) REVERT: C 138 MET cc_start: 0.3957 (ptt) cc_final: 0.3373 (ttt) REVERT: H 109 ARG cc_start: 0.4130 (OUTLIER) cc_final: 0.3315 (pmt-80) REVERT: H 180 LEU cc_start: 0.5587 (mt) cc_final: 0.5301 (mt) REVERT: I 155 TRP cc_start: 0.5717 (m100) cc_final: 0.4924 (m100) REVERT: K 49 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4290 (ppp) REVERT: M 46 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6297 (mp) REVERT: P 23 LYS cc_start: 0.7416 (tttp) cc_final: 0.7093 (tttp) REVERT: P 94 MET cc_start: 0.6286 (tmm) cc_final: 0.5531 (tmm) outliers start: 94 outliers final: 59 residues processed: 429 average time/residue: 0.2308 time to fit residues: 163.3764 Evaluate side-chains 402 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 1.431 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 712 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1111 VAL 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 106 ASP Chi-restraints excluded: chain H residue 109 ARG Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 73 THR 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 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 51 ILE 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: 2.9990 chunk 356 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 361 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 343 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1089 GLN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 M 66 GLN O 37 GLN O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104871 restraints weight = 63421.205| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.05 r_work: 0.3197 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 39995 Z= 0.165 Angle : 0.606 16.827 54505 Z= 0.305 Chirality : 0.047 0.649 6202 Planarity : 0.004 0.052 6931 Dihedral : 5.431 52.186 6078 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 2.27 % Allowed : 13.77 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4894 helix: 2.09 (0.20), residues: 696 sheet: 0.53 (0.13), residues: 1554 loop : -1.26 (0.11), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 966 TYR 0.039 0.001 TYR A 334 PHE 0.021 0.002 PHE C 321 TRP 0.013 0.001 TRP P 84 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00401 (39902) covalent geometry : angle 0.58272 (54283) SS BOND : bond 0.00527 ( 57) SS BOND : angle 1.44030 ( 114) hydrogen bonds : bond 0.05126 ( 1392) hydrogen bonds : angle 5.17773 ( 3792) link_BETA1-4 : bond 0.00266 ( 12) link_BETA1-4 : angle 1.29767 ( 36) link_NAG-ASN : bond 0.00481 ( 24) link_NAG-ASN : angle 4.18431 ( 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 453 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 355 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8341 (mm) REVERT: A 116 CYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5317 (m) REVERT: A 143 TYR cc_start: 0.4734 (OUTLIER) cc_final: 0.2546 (m-80) REVERT: B 791 ASP cc_start: 0.8076 (t0) cc_final: 0.7738 (t0) REVERT: C 138 MET cc_start: 0.3966 (ptt) cc_final: 0.3390 (ttt) REVERT: D 124 GLU cc_start: 0.7968 (tt0) cc_final: 0.7725 (tt0) REVERT: D 184 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7492 (mmmm) REVERT: H 61 ASP cc_start: 0.7881 (t70) cc_final: 0.7527 (t0) REVERT: H 109 ARG cc_start: 0.4219 (OUTLIER) cc_final: 0.3328 (pmt-80) REVERT: H 176 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6944 (mt) REVERT: I 155 TRP cc_start: 0.5760 (m100) cc_final: 0.5065 (m100) REVERT: K 40 GLN cc_start: 0.7071 (tm130) cc_final: 0.6373 (tm-30) REVERT: K 49 MET cc_start: 0.5169 (OUTLIER) cc_final: 0.3754 (ppp) REVERT: O 39 LYS cc_start: 0.7455 (mmmt) cc_final: 0.6200 (ttpt) REVERT: O 55 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7190 (tm-30) REVERT: P 3 GLN cc_start: 0.6172 (pm20) cc_final: 0.5933 (pm20) REVERT: P 23 LYS cc_start: 0.7403 (tttp) cc_final: 0.7093 (tttp) REVERT: P 37 TRP cc_start: 0.6339 (m100) cc_final: 0.5956 (m-90) REVERT: P 94 MET cc_start: 0.6287 (tmm) cc_final: 0.5406 (tmm) outliers start: 98 outliers final: 70 residues processed: 433 average time/residue: 0.2316 time to fit residues: 164.3116 Evaluate side-chains 415 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 338 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 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 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 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 B residue 1111 VAL 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 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 706 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain C residue 917 ILE Chi-restraints excluded: chain C residue 1111 VAL Chi-restraints excluded: chain C residue 1119 THR 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 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 11 LEU 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 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 P residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 245 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 158 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 438 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 ASN C 300 ASN ** C 405 ASN ** 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** O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.149565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108759 restraints weight = 63426.948| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.47 r_work: 0.3174 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 39995 Z= 0.202 Angle : 0.635 16.942 54505 Z= 0.319 Chirality : 0.048 0.650 6202 Planarity : 0.004 0.053 6931 Dihedral : 5.504 52.120 6077 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 2.90 % Allowed : 14.18 % Favored : 82.92 % 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: 2.01 (0.20), residues: 697 sheet: 0.47 (0.13), residues: 1563 loop : -1.28 (0.11), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 966 TYR 0.028 0.002 TYR A 334 PHE 0.026 0.002 PHE C 321 TRP 0.013 0.001 TRP P 84 HIS 0.010 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00496 (39902) covalent geometry : angle 0.61251 (54283) SS BOND : bond 0.00509 ( 57) SS BOND : angle 1.55188 ( 114) hydrogen bonds : bond 0.05537 ( 1392) hydrogen bonds : angle 5.21719 ( 3792) link_BETA1-4 : bond 0.00288 ( 12) link_BETA1-4 : angle 1.35667 ( 36) link_NAG-ASN : bond 0.00466 ( 24) link_NAG-ASN : angle 4.20504 ( 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 475 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 350 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5836 (OUTLIER) cc_final: 0.5412 (m) REVERT: A 143 TYR cc_start: 0.4884 (OUTLIER) cc_final: 0.2545 (m-80) REVERT: A 1094 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8433 (pp20) REVERT: B 791 ASP cc_start: 0.8039 (t0) cc_final: 0.7771 (t0) REVERT: C 138 MET cc_start: 0.3840 (ptt) cc_final: 0.3443 (ttt) REVERT: C 1125 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7857 (mm110) REVERT: D 90 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8591 (tt0) REVERT: D 124 GLU cc_start: 0.7961 (tt0) cc_final: 0.7717 (tt0) REVERT: D 184 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7630 (mmmm) REVERT: H 61 ASP cc_start: 0.7877 (t70) cc_final: 0.7540 (t0) REVERT: H 109 ARG cc_start: 0.4357 (OUTLIER) cc_final: 0.2644 (pmt-80) REVERT: H 176 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6994 (mt) REVERT: I 155 TRP cc_start: 0.5856 (m100) cc_final: 0.5259 (m100) REVERT: K 49 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4299 (ppp) REVERT: M 46 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6286 (mp) REVERT: P 37 TRP cc_start: 0.6352 (m100) cc_final: 0.6050 (m-90) REVERT: P 60 ARG cc_start: 0.7364 (mpt90) cc_final: 0.7139 (mpt-90) REVERT: P 94 MET cc_start: 0.6290 (tmm) cc_final: 0.5706 (tmm) outliers start: 125 outliers final: 95 residues processed: 451 average time/residue: 0.2222 time to fit residues: 165.8372 Evaluate side-chains 443 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 339 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 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 959 VAL 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 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 410 ASP 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 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 1111 VAL 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 712 VAL Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 917 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 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 G residue 85 VAL 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 H residue 207 THR 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: 0.6980 chunk 49 optimal weight: 4.9990 chunk 356 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 237 optimal weight: 3.9990 chunk 288 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** 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 ** 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 = 0.4047 r_free = 0.4047 target = 0.151058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106354 restraints weight = 63441.348| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.09 r_work: 0.3216 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39995 Z= 0.143 Angle : 0.595 16.436 54505 Z= 0.298 Chirality : 0.046 0.637 6202 Planarity : 0.004 0.053 6931 Dihedral : 5.303 52.532 6077 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.58 % Favored : 95.38 % Rotamer: Outliers : 2.72 % Allowed : 14.88 % Favored : 82.40 % 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: -0.23 (0.12), residues: 4894 helix: 2.14 (0.21), residues: 696 sheet: 0.51 (0.13), residues: 1562 loop : -1.25 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 966 TYR 0.027 0.001 TYR L 49 PHE 0.021 0.001 PHE B 77 TRP 0.011 0.001 TRP P 84 HIS 0.007 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00342 (39902) covalent geometry : angle 0.57315 (54283) SS BOND : bond 0.00483 ( 57) SS BOND : angle 1.31429 ( 114) hydrogen bonds : bond 0.04876 ( 1392) hydrogen bonds : angle 5.07128 ( 3792) link_BETA1-4 : bond 0.00298 ( 12) link_BETA1-4 : angle 1.34917 ( 36) link_NAG-ASN : bond 0.00451 ( 24) link_NAG-ASN : angle 4.07840 ( 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: 117 poor density : 345 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8280 (mm) REVERT: A 116 CYS cc_start: 0.5684 (OUTLIER) cc_final: 0.5239 (m) REVERT: A 143 TYR cc_start: 0.4874 (OUTLIER) cc_final: 0.2457 (m-80) REVERT: A 1094 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: B 125 PHE cc_start: 0.6200 (p90) cc_final: 0.5488 (t80) REVERT: B 791 ASP cc_start: 0.8028 (t0) cc_final: 0.7677 (t0) REVERT: B 967 LEU cc_start: 0.7638 (tp) cc_final: 0.7415 (tp) REVERT: C 138 MET cc_start: 0.3787 (ptt) cc_final: 0.3402 (ttt) REVERT: C 1125 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7910 (mm110) REVERT: D 184 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7493 (mmmm) REVERT: H 61 ASP cc_start: 0.7947 (t70) cc_final: 0.7628 (t0) REVERT: H 109 ARG cc_start: 0.4335 (OUTLIER) cc_final: 0.2586 (pmt-80) REVERT: H 150 LYS cc_start: 0.7497 (mtpp) cc_final: 0.6994 (mtmm) REVERT: H 176 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6957 (mt) REVERT: I 155 TRP cc_start: 0.5672 (m100) cc_final: 0.5113 (m100) REVERT: K 49 MET cc_start: 0.5204 (OUTLIER) cc_final: 0.3801 (ppp) REVERT: M 46 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6335 (mp) REVERT: M 69 VAL cc_start: 0.3672 (m) cc_final: 0.3458 (p) REVERT: O 39 LYS cc_start: 0.7445 (mmmt) cc_final: 0.6358 (tmmt) REVERT: P 3 GLN cc_start: 0.6152 (pm20) cc_final: 0.5930 (pm20) REVERT: P 94 MET cc_start: 0.6167 (tmm) cc_final: 0.5584 (tmm) REVERT: P 111 TRP cc_start: 0.7169 (OUTLIER) cc_final: 0.5110 (m-10) outliers start: 117 outliers final: 81 residues processed: 440 average time/residue: 0.2283 time to fit residues: 166.2717 Evaluate side-chains 428 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 337 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 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 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 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 559 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 416 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE 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 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 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 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 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 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 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: 2.9990 chunk 305 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 326 optimal weight: 0.0170 chunk 9 optimal weight: 0.0970 chunk 467 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 365 optimal weight: 0.6980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 101 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** O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.154956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109864 restraints weight = 63449.056| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.06 r_work: 0.3291 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 39995 Z= 0.096 Angle : 0.545 15.253 54505 Z= 0.273 Chirality : 0.044 0.605 6202 Planarity : 0.004 0.052 6931 Dihedral : 4.834 52.510 6077 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 1.95 % Allowed : 15.65 % Favored : 82.40 % 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: -0.07 (0.12), residues: 4894 helix: 2.37 (0.21), residues: 694 sheet: 0.56 (0.13), residues: 1589 loop : -1.15 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 966 TYR 0.031 0.001 TYR A 334 PHE 0.021 0.001 PHE B 77 TRP 0.011 0.001 TRP J 35 HIS 0.005 0.000 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00215 (39902) covalent geometry : angle 0.52472 (54283) SS BOND : bond 0.00480 ( 57) SS BOND : angle 1.14769 ( 114) hydrogen bonds : bond 0.03776 ( 1392) hydrogen bonds : angle 4.79821 ( 3792) link_BETA1-4 : bond 0.00355 ( 12) link_BETA1-4 : angle 1.36689 ( 36) link_NAG-ASN : bond 0.00478 ( 24) link_NAG-ASN : angle 3.79474 ( 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 459 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5468 (OUTLIER) cc_final: 0.5047 (m) REVERT: A 143 TYR cc_start: 0.4678 (OUTLIER) cc_final: 0.2177 (m-80) REVERT: A 1094 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8246 (pp20) REVERT: B 102 LEU cc_start: 0.7550 (mp) cc_final: 0.7205 (tt) REVERT: B 125 PHE cc_start: 0.6306 (p90) cc_final: 0.5637 (t80) REVERT: B 791 ASP cc_start: 0.7852 (t0) cc_final: 0.7506 (t0) REVERT: B 967 LEU cc_start: 0.7672 (tp) cc_final: 0.7466 (tp) REVERT: C 138 MET cc_start: 0.3720 (ptt) cc_final: 0.3396 (ttt) REVERT: C 488 TYR cc_start: 0.6727 (t80) cc_final: 0.6470 (t80) REVERT: C 1125 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7947 (mm110) REVERT: D 71 ASP cc_start: 0.8329 (t0) cc_final: 0.8095 (m-30) REVERT: D 184 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7429 (mmmm) REVERT: H 61 ASP cc_start: 0.7878 (t70) cc_final: 0.7570 (t0) REVERT: H 109 ARG cc_start: 0.4336 (OUTLIER) cc_final: 0.2585 (pmt-80) REVERT: H 150 LYS cc_start: 0.7573 (mtpp) cc_final: 0.7056 (mtmm) REVERT: I 38 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8133 (ptp-170) REVERT: I 124 PRO cc_start: 0.5284 (Cg_exo) cc_final: 0.4938 (Cg_endo) REVERT: I 155 TRP cc_start: 0.5432 (m100) cc_final: 0.4955 (m100) REVERT: K 49 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.3747 (ppp) REVERT: M 46 LEU cc_start: 0.6609 (mt) cc_final: 0.6310 (mp) REVERT: M 113 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7519 (mtm-85) REVERT: O 39 LYS cc_start: 0.7455 (mmmt) cc_final: 0.6384 (tmmt) REVERT: P 3 GLN cc_start: 0.6216 (pm20) cc_final: 0.6000 (pm20) REVERT: P 94 MET cc_start: 0.6124 (tmm) cc_final: 0.5524 (tmm) REVERT: P 111 TRP cc_start: 0.7195 (OUTLIER) cc_final: 0.5401 (m-10) outliers start: 84 outliers final: 62 residues processed: 441 average time/residue: 0.2302 time to fit residues: 166.7239 Evaluate side-chains 414 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1094 GLU 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 559 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain B residue 895 THR 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 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 552 ILE Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 768 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 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 109 ARG Chi-restraints excluded: chain H residue 147 VAL 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 M residue 119 VAL Chi-restraints excluded: chain O residue 4 MET 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: 1.9990 chunk 283 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 123 optimal weight: 0.0770 chunk 160 optimal weight: 1.9990 chunk 464 optimal weight: 20.0000 chunk 316 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 338 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN B 993 GLN C 300 ASN ** 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 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.152084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.106480 restraints weight = 63285.161| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.96 r_work: 0.3228 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 39995 Z= 0.165 Angle : 0.595 15.900 54505 Z= 0.299 Chirality : 0.046 0.614 6202 Planarity : 0.004 0.057 6931 Dihedral : 4.994 52.875 6077 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.62 % Favored : 95.34 % Rotamer: Outliers : 2.25 % Allowed : 15.58 % 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: -0.11 (0.12), residues: 4894 helix: 2.24 (0.20), residues: 695 sheet: 0.55 (0.13), residues: 1578 loop : -1.16 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 966 TYR 0.039 0.001 TYR A 334 PHE 0.020 0.001 PHE B 77 TRP 0.017 0.001 TRP K 111 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00404 (39902) covalent geometry : angle 0.57179 (54283) SS BOND : bond 0.00526 ( 57) SS BOND : angle 1.83738 ( 114) hydrogen bonds : bond 0.04766 ( 1392) hydrogen bonds : angle 4.93404 ( 3792) link_BETA1-4 : bond 0.00277 ( 12) link_BETA1-4 : angle 1.34757 ( 36) link_NAG-ASN : bond 0.00464 ( 24) link_NAG-ASN : angle 3.94175 ( 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 441 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 344 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5650 (OUTLIER) cc_final: 0.5244 (m) REVERT: A 143 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.2253 (m-80) REVERT: A 1094 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8333 (pp20) REVERT: B 125 PHE cc_start: 0.6390 (p90) cc_final: 0.5691 (t80) REVERT: B 791 ASP cc_start: 0.7956 (t0) cc_final: 0.7590 (t0) REVERT: B 967 LEU cc_start: 0.7683 (tp) cc_final: 0.7459 (tp) REVERT: C 138 MET cc_start: 0.3638 (ptt) cc_final: 0.3297 (ttt) REVERT: C 1125 GLN cc_start: 0.8202 (mm-40) cc_final: 0.7947 (mm110) REVERT: D 184 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7477 (mmmm) REVERT: H 61 ASP cc_start: 0.7937 (t70) cc_final: 0.7632 (t0) REVERT: H 150 LYS cc_start: 0.7587 (mtpp) cc_final: 0.7071 (mtmm) REVERT: H 176 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6638 (mt) REVERT: I 38 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8145 (ptp-170) REVERT: I 69 MET cc_start: 0.9030 (mtt) cc_final: 0.8639 (mtt) REVERT: I 155 TRP cc_start: 0.5578 (m100) cc_final: 0.5100 (m100) REVERT: K 49 MET cc_start: 0.5193 (OUTLIER) cc_final: 0.4321 (ppp) REVERT: M 46 LEU cc_start: 0.6669 (mt) cc_final: 0.6356 (mp) REVERT: O 39 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6361 (tmmt) REVERT: P 3 GLN cc_start: 0.6204 (pm20) cc_final: 0.5999 (pm20) REVERT: P 94 MET cc_start: 0.6183 (tmm) cc_final: 0.5470 (tmm) REVERT: P 111 TRP cc_start: 0.7231 (OUTLIER) cc_final: 0.5233 (m-10) outliers start: 97 outliers final: 82 residues processed: 419 average time/residue: 0.2226 time to fit residues: 153.8263 Evaluate side-chains 430 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 340 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 225 LEU 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 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 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 410 ASP Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 559 VAL 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 1064 ILE Chi-restraints excluded: chain B residue 1111 VAL 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 571 THR Chi-restraints excluded: chain C residue 582 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 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 170 LYS 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 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 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 M residue 119 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE Chi-restraints excluded: chain P residue 71 ILE Chi-restraints excluded: chain P residue 111 TRP Chi-restraints excluded: chain P residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 489 random chunks: chunk 431 optimal weight: 5.9990 chunk 378 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 442 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 206 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 385 optimal weight: 4.9990 chunk 462 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 HIS ** C 405 ASN ** 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** O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.151706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.105820 restraints weight = 63168.123| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 3.02 r_work: 0.3223 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 39995 Z= 0.165 Angle : 0.613 19.658 54505 Z= 0.305 Chirality : 0.047 0.620 6202 Planarity : 0.004 0.058 6931 Dihedral : 5.163 53.151 6077 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 2.39 % Allowed : 15.55 % 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: -0.14 (0.12), residues: 4894 helix: 2.18 (0.20), residues: 697 sheet: 0.53 (0.13), residues: 1583 loop : -1.18 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 966 TYR 0.038 0.001 TYR A 334 PHE 0.022 0.001 PHE B 77 TRP 0.013 0.001 TRP K 111 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00400 (39902) covalent geometry : angle 0.58453 (54283) SS BOND : bond 0.00490 ( 57) SS BOND : angle 1.61128 ( 114) hydrogen bonds : bond 0.04868 ( 1392) hydrogen bonds : angle 4.97503 ( 3792) link_BETA1-4 : bond 0.00290 ( 12) link_BETA1-4 : angle 1.37370 ( 36) link_NAG-ASN : bond 0.00859 ( 24) link_NAG-ASN : angle 4.67055 ( 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 442 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 339 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 CYS cc_start: 0.5648 (OUTLIER) cc_final: 0.5246 (m) REVERT: A 143 TYR cc_start: 0.4801 (OUTLIER) cc_final: 0.2361 (m-80) REVERT: A 361 LYS cc_start: 0.8370 (mttm) cc_final: 0.7940 (tptt) REVERT: A 1094 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8326 (pp20) REVERT: B 125 PHE cc_start: 0.6371 (p90) cc_final: 0.5673 (t80) REVERT: B 791 ASP cc_start: 0.7980 (t0) cc_final: 0.7613 (t0) REVERT: B 967 LEU cc_start: 0.7666 (tp) cc_final: 0.7451 (tp) REVERT: C 138 MET cc_start: 0.3732 (ptt) cc_final: 0.3384 (ttt) REVERT: C 1125 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7961 (mm110) REVERT: D 62 ARG cc_start: 0.8151 (ptp90) cc_final: 0.7856 (ptp90) REVERT: D 184 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7464 (mmmm) REVERT: F 1 GLU cc_start: 0.7848 (tp30) cc_final: 0.7595 (tp30) REVERT: H 61 ASP cc_start: 0.7963 (t70) cc_final: 0.7655 (t0) REVERT: H 150 LYS cc_start: 0.7580 (mtpp) cc_final: 0.7071 (mtmm) REVERT: H 176 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6650 (mt) REVERT: I 38 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8178 (ptp-170) REVERT: I 155 TRP cc_start: 0.5606 (m100) cc_final: 0.5146 (m100) REVERT: K 49 MET cc_start: 0.5231 (OUTLIER) cc_final: 0.4313 (ppp) REVERT: M 46 LEU cc_start: 0.6672 (mt) cc_final: 0.6356 (mp) REVERT: O 39 LYS cc_start: 0.7419 (mmmt) cc_final: 0.6351 (tmmt) REVERT: P 3 GLN cc_start: 0.6195 (pm20) cc_final: 0.5988 (pm20) REVERT: P 94 MET cc_start: 0.6234 (tmm) cc_final: 0.5478 (tmm) REVERT: P 111 TRP cc_start: 0.7220 (OUTLIER) cc_final: 0.5217 (m-10) outliers start: 103 outliers final: 87 residues processed: 420 average time/residue: 0.2331 time to fit residues: 161.3479 Evaluate side-chains 431 residues out of total 4317 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 336 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU 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 225 LEU 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 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 1051 VAL Chi-restraints excluded: chain A residue 1094 GLU 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 410 ASP Chi-restraints excluded: chain B residue 481 GLN Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 712 VAL 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 1111 VAL 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 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 514 THR Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 571 THR Chi-restraints excluded: chain C residue 582 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 110 THR Chi-restraints excluded: chain D residue 170 LYS 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 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 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 37 GLN Chi-restraints excluded: chain M residue 119 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain P residue 51 ILE 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: 0.4980 chunk 191 optimal weight: 1.9990 chunk 25 optimal weight: 0.0070 chunk 487 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 356 optimal weight: 1.9990 chunk 321 optimal weight: 0.5980 chunk 261 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 392 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 GLN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 GLN E 50 GLN E 58 ASN ** E 101 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** O 90 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.154828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.110345 restraints weight = 63382.840| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.04 r_work: 0.3285 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 39995 Z= 0.099 Angle : 0.551 15.041 54505 Z= 0.276 Chirality : 0.044 0.602 6202 Planarity : 0.004 0.057 6931 Dihedral : 4.806 53.511 6077 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 1.97 % Allowed : 15.97 % 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: 0.00 (0.12), residues: 4894 helix: 2.39 (0.20), residues: 695 sheet: 0.61 (0.13), residues: 1587 loop : -1.10 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 966 TYR 0.034 0.001 TYR A 334 PHE 0.023 0.001 PHE B 77 TRP 0.013 0.001 TRP K 111 HIS 0.006 0.001 HIS I 53 Details of bonding type rmsd covalent geometry : bond 0.00224 (39902) covalent geometry : angle 0.52950 (54283) SS BOND : bond 0.00398 ( 57) SS BOND : angle 1.20398 ( 114) hydrogen bonds : bond 0.03808 ( 1392) hydrogen bonds : angle 4.74877 ( 3792) link_BETA1-4 : bond 0.00379 ( 12) link_BETA1-4 : angle 1.40440 ( 36) link_NAG-ASN : bond 0.00529 ( 24) link_NAG-ASN : angle 3.90545 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15956.91 seconds wall clock time: 271 minutes 36.99 seconds (16296.99 seconds total)