Starting phenix.real_space_refine on Sun Aug 24 05:59:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tng_41415/08_2025/8tng_41415.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 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 123 5.16 5 C 10905 2.51 5 N 2966 2.21 5 O 3501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17495 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 910 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: "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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.23, per 1000 atoms: 0.24 Number of scatterers: 17495 At special positions: 0 Unit cell: (135.42, 134.31, 125.43, 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 123 16.00 O 3501 8.00 N 2966 7.00 C 10905 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 197 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 197 " " NAG C 607 " - " ASN C 301 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 197 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 295 " " NAG c 1 " - " ASN E 332 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 386 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 722.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 39 sheets defined 16.9% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.248A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 350 removed outlier: 4.226A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.538A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.469A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 removed outlier: 3.687A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL B 580 " --> pdb=" O LEU B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.951A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.663A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 removed outlier: 4.199A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.101A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 335 through 350 removed outlier: 4.110A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.965A pdb=" N GLY C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.738A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.514A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 596 removed outlier: 3.953A pdb=" N LEU D 581 " --> pdb=" O GLN D 577 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 588 " --> pdb=" O GLU D 584 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.557A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.894A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.924A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.551A pdb=" N LYS E 97 " --> pdb=" O ASN E 94 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 94 through 98' Processing helix chain 'E' and resid 99 through 117 removed outlier: 4.141A pdb=" N THR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 115 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.512A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 removed outlier: 4.320A pdb=" N GLU E 340 " --> pdb=" O ALA E 336 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.578A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.066A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 579 " --> pdb=" O GLN F 575 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 580 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.518A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 removed outlier: 4.194A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.490A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.097A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 274 removed outlier: 3.672A pdb=" N ARG A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 413 through 417 removed outlier: 3.941A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR A 297 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 303 through 308 removed outlier: 4.229A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 removed outlier: 4.436A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 361 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 377 through 378 removed outlier: 4.473A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.805A pdb=" N ILE A 424 " --> pdb=" O MET A 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 35 through 39 Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.109A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.653A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 176 removed outlier: 3.832A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 3.580A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 413 through 417 removed outlier: 4.121A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain 'C' and resid 393 through 395 removed outlier: 4.228A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.525A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 495 through 499 removed outlier: 4.635A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.095A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 172 through 176 removed outlier: 3.684A pdb=" N CYS E 131 " --> pdb=" O LYS E 189 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 274 Processing sheet with id=AC9, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.096A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AD2, first strand: chain 'E' and resid 393 through 395 removed outlier: 4.143A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE E 361 " --> pdb=" O SER E 393 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 377 through 378 removed outlier: 4.419A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.882A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.522A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 45 through 50 removed outlier: 3.786A pdb=" N ARG H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N CYS H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE H 34 " --> pdb=" O CYS H 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.857A pdb=" N MET I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 4.049A pdb=" N GLY I 10 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 47 through 50 removed outlier: 4.857A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.824A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.704A pdb=" N THR J 110 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR J 90 " --> pdb=" O THR J 107 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 45 through 50 removed outlier: 3.697A pdb=" N ARG J 38 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL J 48 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE J 34 " --> pdb=" O CYS J 50 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1101 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: 2.72 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3116 1.33 - 1.46: 6566 1.46 - 1.60: 7981 1.60 - 1.73: 0 1.73 - 1.86: 162 Bond restraints: 17825 Sorted by residual: bond pdb=" C1 NAG E 605 " pdb=" O5 NAG E 605 " ideal model delta sigma weight residual 1.406 1.493 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 1.533 1.472 0.061 1.60e-02 3.91e+03 1.45e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.528 1.472 0.056 1.48e-02 4.57e+03 1.41e+01 bond pdb=" C TYR A 318 " pdb=" O TYR A 318 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" C1 NAG B 701 " pdb=" O5 NAG B 701 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 17820 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 23518 2.31 - 4.63: 572 4.63 - 6.94: 79 6.94 - 9.26: 9 9.26 - 11.57: 3 Bond angle restraints: 24181 Sorted by residual: angle pdb=" CA PHE E 317 " pdb=" C PHE E 317 " pdb=" O PHE E 317 " ideal model delta sigma weight residual 120.32 112.50 7.82 1.11e+00 8.12e-01 4.97e+01 angle pdb=" CA PHE E 317 " pdb=" CB PHE E 317 " pdb=" CG PHE E 317 " ideal model delta sigma weight residual 113.80 120.81 -7.01 1.00e+00 1.00e+00 4.92e+01 angle pdb=" CA CYS E 501 " pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " ideal model delta sigma weight residual 114.40 125.47 -11.07 2.30e+00 1.89e-01 2.31e+01 angle pdb=" CA PHE E 317 " pdb=" C PHE E 317 " pdb=" N TYR E 318 " ideal model delta sigma weight residual 116.32 122.74 -6.42 1.38e+00 5.25e-01 2.17e+01 angle pdb=" N GLU I 30 " pdb=" CA GLU I 30 " pdb=" C GLU I 30 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 ... (remaining 24176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.12: 10530 25.12 - 50.25: 965 50.25 - 75.37: 159 75.37 - 100.50: 33 100.50 - 125.62: 10 Dihedral angle restraints: 11697 sinusoidal: 5675 harmonic: 6022 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -0.15 -85.85 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 11.03 81.97 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 12.78 80.22 1 1.00e+01 1.00e-02 7.97e+01 ... (remaining 11694 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 2893 0.165 - 0.329: 22 0.329 - 0.494: 3 0.494 - 0.658: 3 0.658 - 0.823: 1 Chirality restraints: 2922 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 295 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 637 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.50e+00 ... (remaining 2919 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 301 " 0.001 2.00e-02 2.50e+03 5.15e-02 3.31e+01 pdb=" CG ASN E 301 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASN E 301 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN E 301 " -0.050 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 295 " -0.037 2.00e-02 2.50e+03 3.63e-02 1.64e+01 pdb=" CG ASN A 295 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN A 295 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN A 295 " 0.035 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 637 " -0.039 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN B 637 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 637 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 637 " 0.038 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.040 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 386 2.65 - 3.22: 15651 3.22 - 3.78: 23641 3.78 - 4.34: 30968 4.34 - 4.90: 52616 Nonbonded interactions: 123262 Sorted by model distance: nonbonded pdb=" OG SER H 52 " pdb=" OG SER H 57 " model vdw 2.093 3.040 nonbonded pdb=" OD1 ASN H 96 " pdb=" N ARG H 97 " model vdw 2.126 3.120 nonbonded pdb=" OG SER H 33 " pdb=" O LEU H 51 " model vdw 2.154 3.040 nonbonded pdb=" O ASP B 632 " pdb=" OG SER B 636 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASN J 96 " pdb=" N ARG J 97 " model vdw 2.167 3.120 ... (remaining 123257 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 31 through 607) selection = chain 'C' selection = (chain 'E' and resid 31 through 607) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = (chain 'H' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 113)) selection = (chain 'I' and ((resid 1 and (name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or resid 2 through 113)) selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.590 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 0.087 17943 Z= 0.249 Angle : 0.885 20.225 24493 Z= 0.443 Chirality : 0.057 0.823 2922 Planarity : 0.004 0.063 3009 Dihedral : 18.195 125.624 7689 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.75 % Favored : 88.81 % Rotamer: Outliers : 0.60 % Allowed : 33.66 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.42 (0.18), residues: 2065 helix: -0.78 (0.30), residues: 347 sheet: -0.25 (0.27), residues: 404 loop : -2.44 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 97 TYR 0.023 0.001 TYR C 486 PHE 0.034 0.002 PHE C 233 TRP 0.020 0.001 TRP A 35 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00495 (17825) covalent geometry : angle 0.81642 (24181) SS BOND : bond 0.00533 ( 42) SS BOND : angle 2.56135 ( 84) hydrogen bonds : bond 0.18804 ( 419) hydrogen bonds : angle 6.58830 ( 1101) link_ALPHA1-3 : bond 0.00644 ( 2) link_ALPHA1-3 : angle 2.96422 ( 6) link_BETA1-4 : bond 0.00454 ( 25) link_BETA1-4 : angle 1.35120 ( 75) link_NAG-ASN : bond 0.00530 ( 49) link_NAG-ASN : angle 3.97995 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 301 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 66 HIS cc_start: 0.7730 (m-70) cc_final: 0.7341 (m90) REVERT: E 475 MET cc_start: 0.7575 (tpp) cc_final: 0.7298 (tpp) REVERT: F 639 THR cc_start: 0.7307 (m) cc_final: 0.6928 (p) outliers start: 11 outliers final: 6 residues processed: 310 average time/residue: 0.1474 time to fit residues: 66.0571 Evaluate side-chains 166 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain H residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 188 ASN B 540 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 66 HIS ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 575 GLN F 651 ASN H 39 GLN ** I 100AASN ** 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 = 0.3047 r_free = 0.3047 target = 0.047961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.035654 restraints weight = 96572.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.037137 restraints weight = 51681.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.038168 restraints weight = 35037.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.038885 restraints weight = 27063.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.039347 restraints weight = 22691.755| |-----------------------------------------------------------------------------| r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17943 Z= 0.184 Angle : 0.812 13.015 24493 Z= 0.404 Chirality : 0.048 0.375 2922 Planarity : 0.004 0.064 3009 Dihedral : 11.292 115.590 3832 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.19 % Favored : 88.33 % Rotamer: Outliers : 5.87 % Allowed : 29.00 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.47 (0.19), residues: 2065 helix: -0.64 (0.29), residues: 344 sheet: -0.47 (0.25), residues: 496 loop : -2.59 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 579 TYR 0.012 0.001 TYR A 177 PHE 0.019 0.001 PHE E 382 TRP 0.019 0.001 TRP E 69 HIS 0.004 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00408 (17825) covalent geometry : angle 0.77212 (24181) SS BOND : bond 0.00485 ( 42) SS BOND : angle 1.73825 ( 84) hydrogen bonds : bond 0.04218 ( 419) hydrogen bonds : angle 5.42330 ( 1101) link_ALPHA1-3 : bond 0.00758 ( 2) link_ALPHA1-3 : angle 2.85387 ( 6) link_BETA1-4 : bond 0.00277 ( 25) link_BETA1-4 : angle 1.43278 ( 75) link_NAG-ASN : bond 0.00437 ( 49) link_NAG-ASN : angle 2.96485 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 187 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8935 (m-90) cc_final: 0.8486 (m-90) REVERT: A 95 MET cc_start: 0.9113 (ptm) cc_final: 0.8868 (ptm) REVERT: A 104 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9196 (tmm) REVERT: A 278 THR cc_start: 0.9656 (OUTLIER) cc_final: 0.9395 (p) REVERT: A 325 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8454 (t0) REVERT: A 326 ILE cc_start: 0.9644 (OUTLIER) cc_final: 0.9288 (mm) REVERT: A 368 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8245 (t0) REVERT: A 370 GLU cc_start: 0.8461 (mp0) cc_final: 0.7438 (mp0) REVERT: C 302 ASN cc_start: 0.9202 (OUTLIER) cc_final: 0.8988 (m110) REVERT: C 374 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7680 (t-90) REVERT: D 579 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: D 605 CYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8253 (t) REVERT: D 626 MET cc_start: 0.9289 (mmm) cc_final: 0.9023 (tpp) REVERT: D 654 GLU cc_start: 0.9413 (tp30) cc_final: 0.9171 (tp30) REVERT: E 161 MET cc_start: 0.8563 (mmm) cc_final: 0.8257 (tmm) REVERT: E 185 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7617 (t0) REVERT: E 443 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9267 (tt) REVERT: E 475 MET cc_start: 0.9244 (tpp) cc_final: 0.8993 (tpp) REVERT: F 589 ASP cc_start: 0.9113 (m-30) cc_final: 0.8660 (p0) REVERT: F 626 MET cc_start: 0.9228 (tpp) cc_final: 0.8754 (tpt) REVERT: F 627 THR cc_start: 0.9797 (OUTLIER) cc_final: 0.9512 (p) REVERT: H 3 GLN cc_start: 0.9021 (pm20) cc_final: 0.8347 (pm20) REVERT: H 19 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8978 (tpt90) REVERT: H 76 ASN cc_start: 0.8941 (p0) cc_final: 0.8627 (p0) REVERT: H 100 ASN cc_start: 0.8991 (OUTLIER) cc_final: 0.8425 (t0) REVERT: H 100 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9102 (t) REVERT: I 3 GLN cc_start: 0.9101 (pm20) cc_final: 0.8646 (pm20) REVERT: I 76 ASN cc_start: 0.8924 (p0) cc_final: 0.8602 (p0) REVERT: J 3 GLN cc_start: 0.9250 (pm20) cc_final: 0.8777 (pm20) REVERT: J 37 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (t80) REVERT: J 76 ASN cc_start: 0.8963 (p0) cc_final: 0.8696 (p0) outliers start: 107 outliers final: 39 residues processed: 281 average time/residue: 0.1302 time to fit residues: 55.9161 Evaluate side-chains 208 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 185 ASN Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 174 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 246 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN E 185 ASN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** 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 = 0.2957 r_free = 0.2957 target = 0.043117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.031294 restraints weight = 102311.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.032634 restraints weight = 55523.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033589 restraints weight = 37806.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034250 restraints weight = 29261.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034715 restraints weight = 24570.266| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17943 Z= 0.337 Angle : 0.877 14.255 24493 Z= 0.434 Chirality : 0.048 0.297 2922 Planarity : 0.005 0.065 3009 Dihedral : 10.138 112.713 3830 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.33 % Favored : 88.14 % Rotamer: Outliers : 6.41 % Allowed : 28.45 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.56 (0.18), residues: 2065 helix: -0.60 (0.28), residues: 346 sheet: -0.72 (0.24), residues: 460 loop : -2.54 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 327 TYR 0.013 0.002 TYR A 384 PHE 0.032 0.002 PHE H 27 TRP 0.017 0.002 TRP B 623 HIS 0.005 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00709 (17825) covalent geometry : angle 0.84076 (24181) SS BOND : bond 0.00681 ( 42) SS BOND : angle 1.80409 ( 84) hydrogen bonds : bond 0.04607 ( 419) hydrogen bonds : angle 5.45615 ( 1101) link_ALPHA1-3 : bond 0.00202 ( 2) link_ALPHA1-3 : angle 2.36857 ( 6) link_BETA1-4 : bond 0.00289 ( 25) link_BETA1-4 : angle 1.62418 ( 75) link_NAG-ASN : bond 0.00670 ( 49) link_NAG-ASN : angle 2.88961 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 151 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9248 (ptm) cc_final: 0.8914 (ptm) REVERT: A 104 MET cc_start: 0.9604 (OUTLIER) cc_final: 0.9358 (ptm) REVERT: A 125 LEU cc_start: 0.9761 (tp) cc_final: 0.9479 (mm) REVERT: A 325 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8540 (t0) REVERT: A 326 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9259 (mm) REVERT: B 589 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8824 (p0) REVERT: B 657 GLU cc_start: 0.9624 (tt0) cc_final: 0.9342 (tm-30) REVERT: C 104 MET cc_start: 0.9649 (ptm) cc_final: 0.9214 (ppp) REVERT: C 252 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9387 (mmmt) REVERT: C 369 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9362 (tt) REVERT: C 374 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8288 (t-90) REVERT: C 422 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: D 579 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: D 605 CYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8260 (t) REVERT: D 626 MET cc_start: 0.9320 (mmm) cc_final: 0.8514 (tpp) REVERT: E 104 MET cc_start: 0.9556 (ptm) cc_final: 0.9110 (ppp) REVERT: E 150 MET cc_start: 0.8807 (mpp) cc_final: 0.8248 (mpp) REVERT: E 369 LEU cc_start: 0.9611 (tp) cc_final: 0.9244 (tt) REVERT: E 387 THR cc_start: 0.9316 (OUTLIER) cc_final: 0.8813 (p) REVERT: E 475 MET cc_start: 0.9292 (tpp) cc_final: 0.8933 (tpp) REVERT: F 542 ARG cc_start: 0.8996 (ttm110) cc_final: 0.8758 (ttm110) REVERT: F 626 MET cc_start: 0.9038 (tpp) cc_final: 0.8310 (tpp) REVERT: F 640 GLN cc_start: 0.9494 (OUTLIER) cc_final: 0.9270 (pm20) REVERT: H 2 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7602 (t) REVERT: H 3 GLN cc_start: 0.9000 (pm20) cc_final: 0.8363 (pm20) REVERT: H 76 ASN cc_start: 0.8970 (p0) cc_final: 0.8551 (p0) REVERT: H 100 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: H 100 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.9050 (t) REVERT: I 3 GLN cc_start: 0.9113 (pm20) cc_final: 0.8594 (pm20) REVERT: I 4 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8213 (tt) REVERT: I 23 VAL cc_start: 0.9323 (OUTLIER) cc_final: 0.9108 (p) REVERT: I 55 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9261 (ttmt) REVERT: I 76 ASN cc_start: 0.8982 (p0) cc_final: 0.8588 (p0) REVERT: J 3 GLN cc_start: 0.9240 (pm20) cc_final: 0.8744 (pm20) REVERT: J 37 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8633 (t80) REVERT: J 76 ASN cc_start: 0.9113 (p0) cc_final: 0.8743 (p0) outliers start: 117 outliers final: 55 residues processed: 256 average time/residue: 0.1259 time to fit residues: 49.5441 Evaluate side-chains 206 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 133 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 640 GLN Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 166 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.044030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.032484 restraints weight = 99101.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.033791 restraints weight = 55122.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.034709 restraints weight = 38068.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035339 restraints weight = 29694.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035772 restraints weight = 25075.041| |-----------------------------------------------------------------------------| r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17943 Z= 0.223 Angle : 0.770 14.218 24493 Z= 0.381 Chirality : 0.046 0.295 2922 Planarity : 0.004 0.064 3009 Dihedral : 9.315 111.817 3830 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.85 % Favored : 88.72 % Rotamer: Outliers : 5.43 % Allowed : 28.78 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.37 (0.18), residues: 2065 helix: -0.34 (0.29), residues: 334 sheet: -0.56 (0.24), residues: 461 loop : -2.45 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 500 TYR 0.023 0.001 TYR A 61 PHE 0.014 0.002 PHE H 102 TRP 0.009 0.001 TRP F 623 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00480 (17825) covalent geometry : angle 0.73334 (24181) SS BOND : bond 0.00434 ( 42) SS BOND : angle 1.75056 ( 84) hydrogen bonds : bond 0.03986 ( 419) hydrogen bonds : angle 5.09184 ( 1101) link_ALPHA1-3 : bond 0.00693 ( 2) link_ALPHA1-3 : angle 2.67962 ( 6) link_BETA1-4 : bond 0.00189 ( 25) link_BETA1-4 : angle 1.32854 ( 75) link_NAG-ASN : bond 0.00414 ( 49) link_NAG-ASN : angle 2.71418 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 145 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9158 (ptm) cc_final: 0.8834 (ptm) REVERT: A 104 MET cc_start: 0.9638 (OUTLIER) cc_final: 0.9371 (ptm) REVERT: A 125 LEU cc_start: 0.9727 (tp) cc_final: 0.9472 (mm) REVERT: A 150 MET cc_start: 0.8053 (mtm) cc_final: 0.7679 (mpp) REVERT: A 325 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8549 (t0) REVERT: A 326 ILE cc_start: 0.9646 (OUTLIER) cc_final: 0.9287 (mm) REVERT: A 475 MET cc_start: 0.8980 (tpp) cc_final: 0.8581 (tpt) REVERT: B 535 MET cc_start: 0.9584 (mmt) cc_final: 0.9363 (mmt) REVERT: B 589 ASP cc_start: 0.9109 (m-30) cc_final: 0.8833 (p0) REVERT: B 602 LEU cc_start: 0.9318 (mt) cc_final: 0.8830 (pp) REVERT: B 657 GLU cc_start: 0.9631 (tt0) cc_final: 0.9348 (tm-30) REVERT: C 95 MET cc_start: 0.9245 (ptm) cc_final: 0.8573 (tmm) REVERT: C 104 MET cc_start: 0.9629 (ptm) cc_final: 0.9172 (ppp) REVERT: C 121 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9090 (tptp) REVERT: C 258 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8832 (pt0) REVERT: C 374 HIS cc_start: 0.8520 (OUTLIER) cc_final: 0.8146 (t-90) REVERT: C 422 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8734 (mp10) REVERT: D 579 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8001 (mtm-85) REVERT: D 605 CYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8010 (t) REVERT: D 626 MET cc_start: 0.9331 (mmm) cc_final: 0.8477 (tpp) REVERT: E 104 MET cc_start: 0.9605 (ptm) cc_final: 0.9181 (ppp) REVERT: E 150 MET cc_start: 0.8645 (mpp) cc_final: 0.8434 (mpp) REVERT: E 369 LEU cc_start: 0.9603 (tp) cc_final: 0.9310 (tt) REVERT: E 387 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8848 (p) REVERT: E 422 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: E 434 MET cc_start: 0.8449 (tmm) cc_final: 0.8187 (tmm) REVERT: F 542 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8790 (ttm110) REVERT: F 626 MET cc_start: 0.8943 (tpp) cc_final: 0.8233 (tpp) REVERT: H 3 GLN cc_start: 0.9027 (pm20) cc_final: 0.8348 (pm20) REVERT: H 4 LEU cc_start: 0.8104 (mt) cc_final: 0.7333 (tp) REVERT: H 19 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.9207 (tpt90) REVERT: H 76 ASN cc_start: 0.9070 (p0) cc_final: 0.8677 (p0) REVERT: H 100 THR cc_start: 0.9401 (OUTLIER) cc_final: 0.9078 (t) REVERT: I 3 GLN cc_start: 0.9119 (pm20) cc_final: 0.8583 (pm20) REVERT: I 4 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8141 (tt) REVERT: I 23 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9220 (p) REVERT: I 55 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9271 (ttpt) REVERT: I 76 ASN cc_start: 0.9083 (p0) cc_final: 0.8633 (p0) REVERT: I 89 VAL cc_start: 0.9755 (OUTLIER) cc_final: 0.9551 (p) REVERT: J 3 GLN cc_start: 0.9251 (pm20) cc_final: 0.8688 (pm20) REVERT: J 4 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8333 (tt) REVERT: J 37 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8602 (t80) REVERT: J 76 ASN cc_start: 0.9176 (p0) cc_final: 0.8783 (p0) REVERT: J 87 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8886 (m) outliers start: 99 outliers final: 57 residues processed: 235 average time/residue: 0.1121 time to fit residues: 40.0475 Evaluate side-chains 212 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 136 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 422 GLN Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 86 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 113 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 chunk 206 optimal weight: 0.3980 chunk 77 optimal weight: 7.9990 chunk 198 optimal weight: 0.6980 chunk 180 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN E 170 GLN E 188 ASN ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.044710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.033014 restraints weight = 98520.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.034367 restraints weight = 54018.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.035340 restraints weight = 37257.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.035918 restraints weight = 29076.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.036409 restraints weight = 24974.498| |-----------------------------------------------------------------------------| r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17943 Z= 0.122 Angle : 0.738 14.143 24493 Z= 0.364 Chirality : 0.046 0.265 2922 Planarity : 0.004 0.060 3009 Dihedral : 8.630 109.176 3829 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.88 % Favored : 89.69 % Rotamer: Outliers : 4.33 % Allowed : 28.51 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.23 (0.18), residues: 2065 helix: -0.41 (0.29), residues: 352 sheet: -0.37 (0.24), residues: 497 loop : -2.42 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 542 TYR 0.028 0.001 TYR A 61 PHE 0.025 0.001 PHE J 27 TRP 0.010 0.001 TRP A 338 HIS 0.004 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00274 (17825) covalent geometry : angle 0.70558 (24181) SS BOND : bond 0.00373 ( 42) SS BOND : angle 1.48271 ( 84) hydrogen bonds : bond 0.03439 ( 419) hydrogen bonds : angle 4.76862 ( 1101) link_ALPHA1-3 : bond 0.00925 ( 2) link_ALPHA1-3 : angle 2.79667 ( 6) link_BETA1-4 : bond 0.00405 ( 25) link_BETA1-4 : angle 1.14427 ( 75) link_NAG-ASN : bond 0.00398 ( 49) link_NAG-ASN : angle 2.59034 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 169 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8883 (t) REVERT: A 95 MET cc_start: 0.9186 (ptm) cc_final: 0.8832 (ptm) REVERT: A 104 MET cc_start: 0.9639 (OUTLIER) cc_final: 0.9173 (ptm) REVERT: A 125 LEU cc_start: 0.9676 (tp) cc_final: 0.9413 (mm) REVERT: A 369 LEU cc_start: 0.9596 (tp) cc_final: 0.9389 (tt) REVERT: A 475 MET cc_start: 0.9106 (tpp) cc_final: 0.8675 (tpp) REVERT: A 478 ASN cc_start: 0.9422 (m-40) cc_final: 0.8895 (p0) REVERT: B 654 GLU cc_start: 0.9628 (tm-30) cc_final: 0.9349 (pp20) REVERT: B 655 LYS cc_start: 0.9736 (tppt) cc_final: 0.9387 (ptpt) REVERT: C 95 MET cc_start: 0.9233 (ptm) cc_final: 0.8481 (tmm) REVERT: C 104 MET cc_start: 0.9627 (ptm) cc_final: 0.9409 (ppp) REVERT: C 121 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9100 (tptp) REVERT: C 161 MET cc_start: 0.9076 (mmm) cc_final: 0.8700 (tmm) REVERT: C 374 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7560 (t-90) REVERT: C 475 MET cc_start: 0.8514 (tpt) cc_final: 0.8021 (tpt) REVERT: D 579 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.7647 (mtm-85) REVERT: D 605 CYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8032 (t) REVERT: D 626 MET cc_start: 0.9329 (mmm) cc_final: 0.8397 (tpp) REVERT: E 104 MET cc_start: 0.9634 (ptm) cc_final: 0.9189 (ppp) REVERT: E 127 VAL cc_start: 0.9687 (OUTLIER) cc_final: 0.9406 (m) REVERT: E 150 MET cc_start: 0.8580 (mpp) cc_final: 0.8364 (mpp) REVERT: E 166 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8537 (ttp80) REVERT: E 369 LEU cc_start: 0.9565 (tp) cc_final: 0.9295 (tt) REVERT: E 434 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8113 (tmm) REVERT: E 475 MET cc_start: 0.9360 (tpp) cc_final: 0.9001 (tpp) REVERT: F 542 ARG cc_start: 0.8979 (ttm110) cc_final: 0.8727 (ttm110) REVERT: H 2 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7497 (t) REVERT: H 3 GLN cc_start: 0.8983 (pm20) cc_final: 0.8335 (pm20) REVERT: H 4 LEU cc_start: 0.8165 (mt) cc_final: 0.7746 (mt) REVERT: H 19 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8911 (tpt90) REVERT: H 76 ASN cc_start: 0.9105 (p0) cc_final: 0.8663 (p0) REVERT: H 82 MET cc_start: 0.9559 (mmm) cc_final: 0.9342 (mmm) REVERT: H 100 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9049 (t) REVERT: I 3 GLN cc_start: 0.9058 (pm20) cc_final: 0.8496 (pm20) REVERT: I 4 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8009 (tt) REVERT: I 52 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8887 (t) REVERT: I 55 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9230 (ttpt) REVERT: J 3 GLN cc_start: 0.9222 (pm20) cc_final: 0.8614 (pm20) REVERT: J 4 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8429 (tt) REVERT: J 37 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8598 (t80) REVERT: J 76 ASN cc_start: 0.9188 (p0) cc_final: 0.8723 (p0) REVERT: J 87 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8719 (m) outliers start: 79 outliers final: 38 residues processed: 234 average time/residue: 0.1112 time to fit residues: 39.4766 Evaluate side-chains 206 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 152 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 114 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 149 optimal weight: 9.9990 chunk 152 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 117 optimal weight: 10.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN D 575 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032651 restraints weight = 98583.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.033952 restraints weight = 55132.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.034867 restraints weight = 38042.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.035495 restraints weight = 29732.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035943 restraints weight = 25134.778| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17943 Z= 0.206 Angle : 0.761 14.240 24493 Z= 0.372 Chirality : 0.046 0.273 2922 Planarity : 0.004 0.061 3009 Dihedral : 8.484 109.080 3828 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.90 % Favored : 88.67 % Rotamer: Outliers : 4.66 % Allowed : 28.73 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.22 (0.18), residues: 2065 helix: -0.24 (0.29), residues: 343 sheet: -0.38 (0.25), residues: 442 loop : -2.37 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 542 TYR 0.019 0.001 TYR E 39 PHE 0.031 0.002 PHE H 27 TRP 0.012 0.001 TRP A 112 HIS 0.003 0.001 HIS J 61 Details of bonding type rmsd covalent geometry : bond 0.00446 (17825) covalent geometry : angle 0.72657 (24181) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.51858 ( 84) hydrogen bonds : bond 0.03667 ( 419) hydrogen bonds : angle 4.82435 ( 1101) link_ALPHA1-3 : bond 0.00711 ( 2) link_ALPHA1-3 : angle 2.54579 ( 6) link_BETA1-4 : bond 0.00190 ( 25) link_BETA1-4 : angle 1.35858 ( 75) link_NAG-ASN : bond 0.00421 ( 49) link_NAG-ASN : angle 2.65098 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 153 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9216 (ptm) cc_final: 0.8879 (ptm) REVERT: A 104 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9317 (ptm) REVERT: A 125 LEU cc_start: 0.9716 (tp) cc_final: 0.9441 (mm) REVERT: A 258 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8381 (pt0) REVERT: A 475 MET cc_start: 0.9132 (tpp) cc_final: 0.8687 (tpp) REVERT: A 478 ASN cc_start: 0.9421 (m-40) cc_final: 0.8885 (p0) REVERT: B 589 ASP cc_start: 0.9121 (m-30) cc_final: 0.8857 (p0) REVERT: B 602 LEU cc_start: 0.9251 (mt) cc_final: 0.8847 (pp) REVERT: B 654 GLU cc_start: 0.9706 (tm-30) cc_final: 0.9492 (pp20) REVERT: B 657 GLU cc_start: 0.9614 (tt0) cc_final: 0.9374 (tm-30) REVERT: C 95 MET cc_start: 0.9226 (ptm) cc_final: 0.8489 (tmm) REVERT: C 104 MET cc_start: 0.9636 (ptm) cc_final: 0.9281 (ppp) REVERT: C 121 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9148 (tptp) REVERT: C 258 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8771 (pt0) REVERT: C 374 HIS cc_start: 0.8418 (OUTLIER) cc_final: 0.7901 (t-90) REVERT: D 605 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8024 (t) REVERT: D 626 MET cc_start: 0.9313 (mmm) cc_final: 0.8455 (tpp) REVERT: E 104 MET cc_start: 0.9635 (ptm) cc_final: 0.9191 (ppp) REVERT: E 125 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9331 (mm) REVERT: E 369 LEU cc_start: 0.9590 (tp) cc_final: 0.9336 (tt) REVERT: E 434 MET cc_start: 0.8532 (tmm) cc_final: 0.8240 (tmm) REVERT: E 475 MET cc_start: 0.9345 (tpp) cc_final: 0.9089 (tpp) REVERT: F 542 ARG cc_start: 0.9068 (ttm110) cc_final: 0.8811 (ttm110) REVERT: F 603 ILE cc_start: 0.9057 (pt) cc_final: 0.8844 (pt) REVERT: F 626 MET cc_start: 0.8699 (tpp) cc_final: 0.8411 (tpt) REVERT: H 2 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7564 (t) REVERT: H 3 GLN cc_start: 0.9032 (pm20) cc_final: 0.8413 (pm20) REVERT: H 4 LEU cc_start: 0.8272 (mt) cc_final: 0.7815 (mt) REVERT: H 19 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.9104 (tpt90) REVERT: H 76 ASN cc_start: 0.9116 (p0) cc_final: 0.8670 (p0) REVERT: H 100 THR cc_start: 0.9341 (OUTLIER) cc_final: 0.9048 (t) REVERT: I 3 GLN cc_start: 0.9065 (pm20) cc_final: 0.8737 (pm20) REVERT: I 52 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8916 (t) REVERT: I 55 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9327 (ttpt) REVERT: J 3 GLN cc_start: 0.9260 (pm20) cc_final: 0.8701 (pm20) REVERT: J 4 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8287 (tt) REVERT: J 37 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8746 (t80) REVERT: J 45 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.7824 (ptt90) REVERT: J 76 ASN cc_start: 0.9166 (p0) cc_final: 0.8656 (p0) REVERT: J 87 THR cc_start: 0.9216 (OUTLIER) cc_final: 0.8851 (m) outliers start: 85 outliers final: 49 residues processed: 228 average time/residue: 0.1104 time to fit residues: 38.6437 Evaluate side-chains 210 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 145 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 171 optimal weight: 6.9990 chunk 176 optimal weight: 0.0010 chunk 155 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.043862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.032299 restraints weight = 99356.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033634 restraints weight = 54774.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034606 restraints weight = 37576.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.035267 restraints weight = 29160.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.035732 restraints weight = 24498.920| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17943 Z= 0.129 Angle : 0.742 14.267 24493 Z= 0.363 Chirality : 0.046 0.260 2922 Planarity : 0.004 0.060 3009 Dihedral : 8.122 107.685 3828 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.02 % Favored : 89.59 % Rotamer: Outliers : 4.44 % Allowed : 28.78 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.08 (0.18), residues: 2065 helix: -0.13 (0.30), residues: 340 sheet: -0.34 (0.24), residues: 503 loop : -2.34 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 542 TYR 0.014 0.001 TYR E 39 PHE 0.028 0.001 PHE J 27 TRP 0.011 0.001 TRP F 623 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00292 (17825) covalent geometry : angle 0.71126 (24181) SS BOND : bond 0.00368 ( 42) SS BOND : angle 1.48735 ( 84) hydrogen bonds : bond 0.03322 ( 419) hydrogen bonds : angle 4.63567 ( 1101) link_ALPHA1-3 : bond 0.00844 ( 2) link_ALPHA1-3 : angle 2.64542 ( 6) link_BETA1-4 : bond 0.00356 ( 25) link_BETA1-4 : angle 1.13254 ( 75) link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.53513 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 158 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9188 (ptm) cc_final: 0.8823 (ptm) REVERT: A 104 MET cc_start: 0.9531 (OUTLIER) cc_final: 0.9317 (ptm) REVERT: A 125 LEU cc_start: 0.9690 (tp) cc_final: 0.9426 (mm) REVERT: A 150 MET cc_start: 0.7779 (mpp) cc_final: 0.7575 (mpp) REVERT: A 258 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: B 536 THR cc_start: 0.9418 (p) cc_final: 0.9203 (t) REVERT: B 589 ASP cc_start: 0.9096 (m-30) cc_final: 0.8830 (p0) REVERT: B 654 GLU cc_start: 0.9701 (tm-30) cc_final: 0.9487 (pp20) REVERT: B 657 GLU cc_start: 0.9612 (tt0) cc_final: 0.9372 (tm-30) REVERT: C 95 MET cc_start: 0.9250 (ptm) cc_final: 0.8537 (tmm) REVERT: C 104 MET cc_start: 0.9635 (ptm) cc_final: 0.9330 (tmm) REVERT: C 121 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9151 (tptp) REVERT: C 258 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8716 (pt0) REVERT: C 374 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: C 422 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.8569 (mp10) REVERT: C 475 MET cc_start: 0.8571 (tpt) cc_final: 0.8152 (tpt) REVERT: D 542 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8705 (ttp-110) REVERT: D 605 CYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8020 (t) REVERT: D 626 MET cc_start: 0.9281 (mmm) cc_final: 0.8469 (tpp) REVERT: E 104 MET cc_start: 0.9654 (ptm) cc_final: 0.9262 (ppp) REVERT: E 125 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9270 (mm) REVERT: E 166 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8522 (ttp80) REVERT: E 211 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8844 (mp0) REVERT: E 369 LEU cc_start: 0.9568 (tp) cc_final: 0.9337 (tt) REVERT: E 387 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.8798 (p) REVERT: E 434 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8056 (tmm) REVERT: E 475 MET cc_start: 0.9379 (tpp) cc_final: 0.9098 (tpp) REVERT: F 542 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8807 (ttm110) REVERT: F 589 ASP cc_start: 0.9115 (m-30) cc_final: 0.8590 (p0) REVERT: F 626 MET cc_start: 0.8600 (tpp) cc_final: 0.8242 (tpt) REVERT: H 2 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7536 (t) REVERT: H 3 GLN cc_start: 0.8939 (pm20) cc_final: 0.8317 (pm20) REVERT: H 4 LEU cc_start: 0.8319 (mt) cc_final: 0.7867 (mt) REVERT: H 19 ARG cc_start: 0.9411 (OUTLIER) cc_final: 0.8961 (tpt90) REVERT: H 76 ASN cc_start: 0.9147 (p0) cc_final: 0.8675 (p0) REVERT: H 100 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8981 (t) REVERT: I 3 GLN cc_start: 0.9151 (pm20) cc_final: 0.8527 (pm20) REVERT: I 4 LEU cc_start: 0.9333 (mm) cc_final: 0.8841 (mt) REVERT: I 52 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8909 (t) REVERT: I 55 LYS cc_start: 0.9645 (OUTLIER) cc_final: 0.9303 (ttpp) REVERT: J 3 GLN cc_start: 0.9234 (pm20) cc_final: 0.8677 (pm20) REVERT: J 4 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8275 (tt) REVERT: J 37 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8742 (t80) REVERT: J 45 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.7896 (ptt90) REVERT: J 76 ASN cc_start: 0.9219 (p0) cc_final: 0.8696 (p0) REVERT: J 87 THR cc_start: 0.9147 (OUTLIER) cc_final: 0.8787 (m) outliers start: 81 outliers final: 52 residues processed: 226 average time/residue: 0.1174 time to fit residues: 40.7013 Evaluate side-chains 223 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 151 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 43 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.044777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.033067 restraints weight = 100402.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.034395 restraints weight = 56049.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035318 restraints weight = 38620.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.036003 restraints weight = 30275.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.036461 restraints weight = 25487.682| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17943 Z= 0.150 Angle : 0.741 14.192 24493 Z= 0.360 Chirality : 0.045 0.277 2922 Planarity : 0.004 0.057 3009 Dihedral : 7.967 106.688 3828 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.41 % Favored : 89.20 % Rotamer: Outliers : 4.11 % Allowed : 28.89 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.03 (0.19), residues: 2065 helix: 0.23 (0.30), residues: 325 sheet: -0.48 (0.23), residues: 504 loop : -2.28 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 542 TYR 0.010 0.001 TYR E 318 PHE 0.014 0.001 PHE H 102 TRP 0.010 0.001 TRP C 112 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00337 (17825) covalent geometry : angle 0.70905 (24181) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.57387 ( 84) hydrogen bonds : bond 0.03282 ( 419) hydrogen bonds : angle 4.62663 ( 1101) link_ALPHA1-3 : bond 0.00704 ( 2) link_ALPHA1-3 : angle 2.48833 ( 6) link_BETA1-4 : bond 0.00250 ( 25) link_BETA1-4 : angle 1.21513 ( 75) link_NAG-ASN : bond 0.00376 ( 49) link_NAG-ASN : angle 2.53690 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 152 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9205 (ptm) cc_final: 0.8846 (ptm) REVERT: A 104 MET cc_start: 0.9526 (OUTLIER) cc_final: 0.9311 (ptm) REVERT: A 125 LEU cc_start: 0.9699 (tp) cc_final: 0.9422 (mm) REVERT: A 150 MET cc_start: 0.7789 (mpp) cc_final: 0.7567 (mpp) REVERT: A 258 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: A 478 ASN cc_start: 0.9347 (m-40) cc_final: 0.8856 (p0) REVERT: B 536 THR cc_start: 0.9419 (p) cc_final: 0.9202 (t) REVERT: B 589 ASP cc_start: 0.9107 (m-30) cc_final: 0.8811 (p0) REVERT: B 601 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8366 (mmmt) REVERT: B 654 GLU cc_start: 0.9738 (tm-30) cc_final: 0.9321 (tm-30) REVERT: B 657 GLU cc_start: 0.9612 (tt0) cc_final: 0.9368 (tm-30) REVERT: C 95 MET cc_start: 0.9296 (ptm) cc_final: 0.8537 (tmm) REVERT: C 104 MET cc_start: 0.9638 (ptm) cc_final: 0.9326 (tmm) REVERT: C 121 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9155 (tptp) REVERT: C 258 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: C 374 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: C 422 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: C 434 MET cc_start: 0.8816 (ttm) cc_final: 0.8604 (ttm) REVERT: C 475 MET cc_start: 0.8614 (tpt) cc_final: 0.8187 (tpt) REVERT: D 542 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8723 (ttp-110) REVERT: D 605 CYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7990 (t) REVERT: D 626 MET cc_start: 0.9225 (mmm) cc_final: 0.8383 (tpp) REVERT: E 104 MET cc_start: 0.9656 (ptm) cc_final: 0.9248 (ppp) REVERT: E 116 LEU cc_start: 0.9366 (mt) cc_final: 0.8980 (tt) REVERT: E 125 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9263 (mm) REVERT: E 166 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8496 (ttp80) REVERT: E 211 GLU cc_start: 0.9348 (OUTLIER) cc_final: 0.8809 (mp0) REVERT: E 369 LEU cc_start: 0.9558 (tp) cc_final: 0.9349 (tt) REVERT: E 387 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8756 (p) REVERT: F 542 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8844 (ttm110) REVERT: F 589 ASP cc_start: 0.9134 (m-30) cc_final: 0.8639 (p0) REVERT: F 626 MET cc_start: 0.8622 (tpp) cc_final: 0.8243 (tpt) REVERT: H 2 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7591 (t) REVERT: H 3 GLN cc_start: 0.8964 (pm20) cc_final: 0.8334 (pm20) REVERT: H 4 LEU cc_start: 0.8264 (mt) cc_final: 0.7786 (mt) REVERT: H 19 ARG cc_start: 0.9402 (OUTLIER) cc_final: 0.8954 (tpt90) REVERT: H 76 ASN cc_start: 0.9153 (p0) cc_final: 0.8685 (p0) REVERT: H 100 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8973 (t) REVERT: I 3 GLN cc_start: 0.9153 (pm20) cc_final: 0.8544 (pm20) REVERT: I 4 LEU cc_start: 0.9389 (mm) cc_final: 0.8883 (mt) REVERT: I 52 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8892 (t) REVERT: I 55 LYS cc_start: 0.9666 (OUTLIER) cc_final: 0.9334 (ttpp) REVERT: I 76 ASN cc_start: 0.9089 (m-40) cc_final: 0.8510 (t0) REVERT: J 3 GLN cc_start: 0.9215 (pm20) cc_final: 0.8743 (pm20) REVERT: J 4 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8358 (tt) REVERT: J 37 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (t80) REVERT: J 45 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7891 (ptt90) REVERT: J 76 ASN cc_start: 0.9205 (p0) cc_final: 0.8656 (p0) REVERT: J 87 THR cc_start: 0.9176 (OUTLIER) cc_final: 0.8824 (m) outliers start: 75 outliers final: 50 residues processed: 217 average time/residue: 0.1133 time to fit residues: 37.8817 Evaluate side-chains 219 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 150 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 176 optimal weight: 1.9990 chunk 164 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 440 GLN D 590 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.043601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.032032 restraints weight = 101626.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.033312 restraints weight = 56408.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.034230 restraints weight = 39171.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034787 restraints weight = 30594.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.035256 restraints weight = 26320.834| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17943 Z= 0.227 Angle : 0.792 14.340 24493 Z= 0.383 Chirality : 0.045 0.289 2922 Planarity : 0.004 0.057 3009 Dihedral : 8.047 106.530 3827 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.04 % Favored : 88.57 % Rotamer: Outliers : 4.61 % Allowed : 28.51 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.10 (0.18), residues: 2065 helix: 0.25 (0.30), residues: 323 sheet: -0.44 (0.24), residues: 444 loop : -2.32 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 542 TYR 0.011 0.001 TYR A 384 PHE 0.028 0.002 PHE J 27 TRP 0.012 0.001 TRP E 96 HIS 0.003 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00491 (17825) covalent geometry : angle 0.75905 (24181) SS BOND : bond 0.00335 ( 42) SS BOND : angle 1.64583 ( 84) hydrogen bonds : bond 0.03649 ( 419) hydrogen bonds : angle 4.77894 ( 1101) link_ALPHA1-3 : bond 0.00478 ( 2) link_ALPHA1-3 : angle 2.41025 ( 6) link_BETA1-4 : bond 0.00154 ( 25) link_BETA1-4 : angle 1.34562 ( 75) link_NAG-ASN : bond 0.00441 ( 49) link_NAG-ASN : angle 2.63080 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 146 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9217 (ptm) cc_final: 0.8862 (ptm) REVERT: A 104 MET cc_start: 0.9540 (OUTLIER) cc_final: 0.9330 (ptm) REVERT: A 258 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: B 535 MET cc_start: 0.9580 (mmt) cc_final: 0.9361 (mmm) REVERT: B 654 GLU cc_start: 0.9736 (tm-30) cc_final: 0.9522 (pp20) REVERT: B 657 GLU cc_start: 0.9627 (tt0) cc_final: 0.9403 (tm-30) REVERT: C 95 MET cc_start: 0.9255 (ptm) cc_final: 0.8582 (tmm) REVERT: C 104 MET cc_start: 0.9636 (ptm) cc_final: 0.9182 (ppp) REVERT: C 121 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.9158 (tptp) REVERT: C 258 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8660 (pt0) REVERT: C 422 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: C 475 MET cc_start: 0.8585 (tpt) cc_final: 0.8107 (tpt) REVERT: D 542 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8783 (ttp-110) REVERT: D 605 CYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (t) REVERT: D 626 MET cc_start: 0.9241 (mmm) cc_final: 0.8424 (tpp) REVERT: E 104 MET cc_start: 0.9643 (ptm) cc_final: 0.9251 (ppp) REVERT: E 125 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9252 (mm) REVERT: E 150 MET cc_start: 0.8487 (mpp) cc_final: 0.7918 (mpp) REVERT: E 211 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: E 318 TYR cc_start: 0.9149 (m-80) cc_final: 0.8882 (m-80) REVERT: E 475 MET cc_start: 0.9282 (tpp) cc_final: 0.8869 (tpp) REVERT: F 542 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8914 (ttm110) REVERT: F 589 ASP cc_start: 0.9170 (m-30) cc_final: 0.8695 (p0) REVERT: F 626 MET cc_start: 0.8718 (tpp) cc_final: 0.8308 (tpt) REVERT: H 2 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7639 (t) REVERT: H 3 GLN cc_start: 0.8998 (pm20) cc_final: 0.8373 (pm20) REVERT: H 4 LEU cc_start: 0.8313 (mt) cc_final: 0.7828 (mt) REVERT: H 19 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.9169 (tpt90) REVERT: H 76 ASN cc_start: 0.9122 (p0) cc_final: 0.8712 (p0) REVERT: H 100 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9006 (t) REVERT: I 3 GLN cc_start: 0.9246 (pm20) cc_final: 0.8746 (pm20) REVERT: I 55 LYS cc_start: 0.9651 (OUTLIER) cc_final: 0.9362 (ttpp) REVERT: I 76 ASN cc_start: 0.9167 (m-40) cc_final: 0.8572 (t0) REVERT: J 3 GLN cc_start: 0.9299 (pm20) cc_final: 0.8919 (pm20) REVERT: J 4 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8195 (tt) REVERT: J 37 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8721 (t80) REVERT: J 45 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7837 (ptt90) REVERT: J 76 ASN cc_start: 0.9188 (p0) cc_final: 0.8709 (p0) REVERT: J 87 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8838 (m) outliers start: 84 outliers final: 58 residues processed: 218 average time/residue: 0.1149 time to fit residues: 39.0804 Evaluate side-chains 216 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 142 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 96 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 158 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 ASN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.043705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.032265 restraints weight = 98839.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.033589 restraints weight = 54157.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034534 restraints weight = 37190.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035104 restraints weight = 28885.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.035608 restraints weight = 24680.167| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17943 Z= 0.134 Angle : 0.772 14.386 24493 Z= 0.370 Chirality : 0.046 0.268 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.833 105.449 3827 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.12 % Favored : 89.49 % Rotamer: Outliers : 3.73 % Allowed : 29.33 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.98 (0.18), residues: 2065 helix: 0.40 (0.31), residues: 320 sheet: -0.42 (0.24), residues: 484 loop : -2.28 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 542 TYR 0.027 0.001 TYR C 61 PHE 0.011 0.001 PHE J 27 TRP 0.010 0.001 TRP C 112 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00310 (17825) covalent geometry : angle 0.74108 (24181) SS BOND : bond 0.00330 ( 42) SS BOND : angle 1.79746 ( 84) hydrogen bonds : bond 0.03259 ( 419) hydrogen bonds : angle 4.57117 ( 1101) link_ALPHA1-3 : bond 0.00562 ( 2) link_ALPHA1-3 : angle 2.53382 ( 6) link_BETA1-4 : bond 0.00302 ( 25) link_BETA1-4 : angle 1.12356 ( 75) link_NAG-ASN : bond 0.00386 ( 49) link_NAG-ASN : angle 2.50970 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4130 Ramachandran restraints generated. 2065 Oldfield, 0 Emsley, 2065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 153 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.7984 (t80) cc_final: 0.7768 (t80) REVERT: A 95 MET cc_start: 0.9197 (ptm) cc_final: 0.8846 (ptm) REVERT: A 104 MET cc_start: 0.9526 (ttm) cc_final: 0.9300 (ptm) REVERT: A 258 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8402 (pt0) REVERT: B 589 ASP cc_start: 0.9133 (m-30) cc_final: 0.8836 (p0) REVERT: B 654 GLU cc_start: 0.9721 (tm-30) cc_final: 0.9515 (pp20) REVERT: C 95 MET cc_start: 0.9284 (ptm) cc_final: 0.8602 (tmm) REVERT: C 104 MET cc_start: 0.9654 (ptm) cc_final: 0.9210 (ppp) REVERT: C 121 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9176 (tptp) REVERT: C 258 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8706 (pt0) REVERT: C 422 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: C 475 MET cc_start: 0.8523 (tpt) cc_final: 0.8042 (tpt) REVERT: D 542 ARG cc_start: 0.9019 (ttm110) cc_final: 0.8747 (ttp-110) REVERT: D 605 CYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8041 (t) REVERT: D 626 MET cc_start: 0.9233 (mmm) cc_final: 0.8446 (tpp) REVERT: E 104 MET cc_start: 0.9661 (ptm) cc_final: 0.9284 (ppp) REVERT: E 125 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9213 (mm) REVERT: E 150 MET cc_start: 0.8480 (mpp) cc_final: 0.7906 (mpp) REVERT: E 166 ARG cc_start: 0.8715 (ttp80) cc_final: 0.8484 (ttp80) REVERT: E 211 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.8836 (mp0) REVERT: E 271 MET cc_start: 0.7780 (mmm) cc_final: 0.7275 (mmt) REVERT: E 387 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.8867 (p) REVERT: E 434 MET cc_start: 0.8928 (mmt) cc_final: 0.8475 (tpp) REVERT: E 475 MET cc_start: 0.9259 (tpp) cc_final: 0.8866 (tpp) REVERT: F 542 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8851 (ttm110) REVERT: F 589 ASP cc_start: 0.9147 (m-30) cc_final: 0.8649 (p0) REVERT: F 593 LEU cc_start: 0.8809 (pp) cc_final: 0.8522 (pp) REVERT: F 626 MET cc_start: 0.8623 (tpp) cc_final: 0.8202 (tpt) REVERT: H 2 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7607 (t) REVERT: H 3 GLN cc_start: 0.8861 (pm20) cc_final: 0.8199 (pm20) REVERT: H 4 LEU cc_start: 0.8252 (mt) cc_final: 0.7772 (mt) REVERT: H 19 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.9038 (tpt90) REVERT: H 76 ASN cc_start: 0.9146 (p0) cc_final: 0.8723 (p0) REVERT: H 100 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8970 (t) REVERT: I 3 GLN cc_start: 0.9061 (pm20) cc_final: 0.8538 (pm20) REVERT: I 18 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9110 (mm) REVERT: I 55 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9413 (ttpp) REVERT: I 76 ASN cc_start: 0.9138 (m-40) cc_final: 0.8497 (t0) REVERT: J 3 GLN cc_start: 0.9195 (pm20) cc_final: 0.8780 (pm20) REVERT: J 4 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8296 (tt) REVERT: J 45 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.7667 (ptt90) REVERT: J 76 ASN cc_start: 0.9225 (p0) cc_final: 0.8736 (p0) REVERT: J 87 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8831 (m) outliers start: 68 outliers final: 48 residues processed: 210 average time/residue: 0.1200 time to fit residues: 38.5217 Evaluate side-chains 211 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 147 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 422 GLN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 61 TYR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 169 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.031239 restraints weight = 102631.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.032539 restraints weight = 57454.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033477 restraints weight = 39569.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.034029 restraints weight = 30895.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.034511 restraints weight = 26594.866| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17943 Z= 0.194 Angle : 0.793 14.325 24493 Z= 0.381 Chirality : 0.045 0.277 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.873 104.911 3827 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.75 % Favored : 88.86 % Rotamer: Outliers : 3.84 % Allowed : 29.33 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -2.02 (0.18), residues: 2065 helix: 0.41 (0.31), residues: 320 sheet: -0.39 (0.25), residues: 444 loop : -2.28 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 542 TYR 0.018 0.001 TYR C 61 PHE 0.028 0.002 PHE J 27 TRP 0.009 0.001 TRP F 614 HIS 0.004 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00428 (17825) covalent geometry : angle 0.76131 (24181) SS BOND : bond 0.00334 ( 42) SS BOND : angle 1.76211 ( 84) hydrogen bonds : bond 0.03484 ( 419) hydrogen bonds : angle 4.69299 ( 1101) link_ALPHA1-3 : bond 0.00530 ( 2) link_ALPHA1-3 : angle 2.44166 ( 6) link_BETA1-4 : bond 0.00171 ( 25) link_BETA1-4 : angle 1.24867 ( 75) link_NAG-ASN : bond 0.00400 ( 49) link_NAG-ASN : angle 2.56612 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2510.58 seconds wall clock time: 44 minutes 22.58 seconds (2662.58 seconds total)