Starting phenix.real_space_refine on Sun Jun 15 15:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tng_41415/06_2025/8tng_41415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tng_41415/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tng_41415/06_2025/8tng_41415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tng_41415/06_2025/8tng_41415.map" model { file = "/net/cci-nas-00/data/ceres_data/8tng_41415/06_2025/8tng_41415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tng_41415/06_2025/8tng_41415.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.92, per 1000 atoms: 0.62 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: 4.98 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.27 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: 5.19 Time building geometry restraints manager: 5.82 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 505 or resid 601 through 607)) selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 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: 1.250 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: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 40.790 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.350 ------------------------------------------------------------------------------- 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 : 8.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.001 TRP A 35 HIS 0.004 0.001 HIS C 374 PHE 0.034 0.002 PHE C 233 TYR 0.023 0.001 TYR C 486 ARG 0.006 0.000 ARG H 97 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 49) link_NAG-ASN : angle 3.97995 ( 147) link_BETA1-4 : bond 0.00454 ( 25) link_BETA1-4 : angle 1.35120 ( 75) link_ALPHA1-3 : bond 0.00644 ( 2) link_ALPHA1-3 : angle 2.96422 ( 6) hydrogen bonds : bond 0.18804 ( 419) hydrogen bonds : angle 6.58830 ( 1101) SS BOND : bond 0.00533 ( 42) SS BOND : angle 2.56135 ( 84) covalent geometry : bond 0.00495 (17825) covalent geometry : angle 0.81642 (24181) *********************** 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 : 1.999 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: 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: 0.6930 (p) outliers start: 11 outliers final: 6 residues processed: 310 average time/residue: 0.3391 time to fit residues: 151.8530 Evaluate side-chains 168 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 174 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.046311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.034071 restraints weight = 97466.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.035503 restraints weight = 52782.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.036512 restraints weight = 36036.918| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17943 Z= 0.252 Angle : 0.844 13.140 24493 Z= 0.421 Chirality : 0.048 0.374 2922 Planarity : 0.005 0.066 3009 Dihedral : 11.469 115.791 3832 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.57 % Favored : 87.94 % Rotamer: Outliers : 6.47 % Allowed : 28.34 % Favored : 65.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.18), residues: 2065 helix: -0.89 (0.28), residues: 367 sheet: -0.45 (0.25), residues: 454 loop : -2.58 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 69 HIS 0.005 0.001 HIS H 61 PHE 0.022 0.002 PHE E 382 TYR 0.011 0.002 TYR F 643 ARG 0.008 0.001 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 49) link_NAG-ASN : angle 3.03020 ( 147) link_BETA1-4 : bond 0.00227 ( 25) link_BETA1-4 : angle 1.45305 ( 75) link_ALPHA1-3 : bond 0.00863 ( 2) link_ALPHA1-3 : angle 2.82240 ( 6) hydrogen bonds : bond 0.04553 ( 419) hydrogen bonds : angle 5.53310 ( 1101) SS BOND : bond 0.00447 ( 42) SS BOND : angle 1.83277 ( 84) covalent geometry : bond 0.00548 (17825) covalent geometry : angle 0.80372 (24181) *********************** 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 297 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 179 time to evaluate : 1.912 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: 0.9118 (ptm) cc_final: 0.8858 (ptm) REVERT: A 104 MET cc_start: 0.9592 (OUTLIER) cc_final: 0.9109 (ptm) REVERT: A 125 LEU cc_start: 0.9697 (tp) cc_final: 0.9457 (mm) REVERT: A 278 THR cc_start: 0.9665 (OUTLIER) cc_final: 0.9404 (p) REVERT: A 325 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8351 (t0) REVERT: A 326 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9461 (mm) REVERT: B 657 GLU cc_start: 0.9645 (tt0) cc_final: 0.9337 (tm-30) REVERT: C 104 MET cc_start: 0.9614 (OUTLIER) cc_final: 0.9052 (ppp) REVERT: C 374 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7844 (t-90) REVERT: C 479 TRP cc_start: 0.9341 (m-10) cc_final: 0.8236 (m-10) REVERT: D 579 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8019 (mtm-85) REVERT: D 626 MET cc_start: 0.9286 (mmm) cc_final: 0.8949 (tpp) REVERT: E 104 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9281 (ptm) REVERT: E 161 MET cc_start: 0.8538 (mmm) cc_final: 0.8239 (tmm) REVERT: E 296 CYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5504 (m) REVERT: E 369 LEU cc_start: 0.9333 (tp) cc_final: 0.9002 (tt) REVERT: E 475 MET cc_start: 0.9250 (tpp) cc_final: 0.9011 (tpp) REVERT: F 589 ASP cc_start: 0.9078 (m-30) cc_final: 0.8628 (p0) REVERT: F 626 MET cc_start: 0.9243 (tpp) cc_final: 0.8809 (tpt) REVERT: F 627 THR cc_start: 0.9807 (OUTLIER) cc_final: 0.9470 (p) REVERT: F 657 GLU cc_start: 0.9420 (tt0) cc_final: 0.8954 (pt0) REVERT: H 3 GLN cc_start: 0.9143 (pm20) cc_final: 0.8477 (pm20) REVERT: H 19 ARG cc_start: 0.9389 (OUTLIER) cc_final: 0.9177 (tpt90) REVERT: H 76 ASN cc_start: 0.8883 (p0) cc_final: 0.8576 (p0) REVERT: H 100 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8459 (m-40) REVERT: H 100 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9124 (t) REVERT: I 3 GLN cc_start: 0.9123 (pm20) cc_final: 0.8705 (pm20) REVERT: I 76 ASN cc_start: 0.8900 (p0) cc_final: 0.8584 (p0) REVERT: I 96 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7870 (p0) REVERT: J 3 GLN cc_start: 0.9305 (pm20) cc_final: 0.8827 (pm20) REVERT: J 37 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8711 (t80) REVERT: J 76 ASN cc_start: 0.8926 (p0) cc_final: 0.8681 (p0) outliers start: 118 outliers final: 42 residues processed: 282 average time/residue: 0.2863 time to fit residues: 122.5564 Evaluate side-chains 209 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 153 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 C residue 100 MET Chi-restraints excluded: chain C residue 104 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 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 583 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 648 GLU 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 104 MET Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 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 F residue 573 ILE Chi-restraints excluded: chain F residue 575 GLN 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 100 ASN Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 37 PHE 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 195 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 577 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 651 ASN ** I 56 ASN ** 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 = 0.3003 r_free = 0.3003 target = 0.045264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.033269 restraints weight = 97500.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.034653 restraints weight = 53143.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.035646 restraints weight = 36480.066| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17943 Z= 0.210 Angle : 0.778 13.883 24493 Z= 0.387 Chirality : 0.047 0.265 2922 Planarity : 0.004 0.063 3009 Dihedral : 10.070 112.206 3831 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.27 % Favored : 89.20 % Rotamer: Outliers : 5.26 % Allowed : 29.11 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.18), residues: 2065 helix: -0.79 (0.28), residues: 367 sheet: -0.48 (0.24), residues: 491 loop : -2.62 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 628 HIS 0.003 0.001 HIS H 61 PHE 0.034 0.002 PHE B 519 TYR 0.011 0.001 TYR D 638 ARG 0.006 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 49) link_NAG-ASN : angle 2.70419 ( 147) link_BETA1-4 : bond 0.00251 ( 25) link_BETA1-4 : angle 1.37234 ( 75) link_ALPHA1-3 : bond 0.00652 ( 2) link_ALPHA1-3 : angle 2.59975 ( 6) hydrogen bonds : bond 0.04102 ( 419) hydrogen bonds : angle 5.19259 ( 1101) SS BOND : bond 0.00529 ( 42) SS BOND : angle 1.59884 ( 84) covalent geometry : bond 0.00452 (17825) covalent geometry : angle 0.74321 (24181) *********************** 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 261 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 165 time to evaluate : 1.808 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: 0.9123 (ptm) cc_final: 0.8791 (ptm) REVERT: A 104 MET cc_start: 0.9455 (OUTLIER) cc_final: 0.9241 (ptm) REVERT: A 125 LEU cc_start: 0.9729 (tp) cc_final: 0.9479 (mm) REVERT: A 150 MET cc_start: 0.8050 (mtm) cc_final: 0.7626 (mpp) REVERT: A 258 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8584 (pt0) REVERT: A 278 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.9212 (p) REVERT: A 325 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 326 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9444 (mm) REVERT: A 369 LEU cc_start: 0.9587 (tp) cc_final: 0.9383 (tt) REVERT: B 535 MET cc_start: 0.9616 (mmt) cc_final: 0.9387 (mmt) REVERT: B 589 ASP cc_start: 0.9052 (m-30) cc_final: 0.8688 (p0) REVERT: B 657 GLU cc_start: 0.9624 (tt0) cc_final: 0.9335 (tm-30) REVERT: C 104 MET cc_start: 0.9635 (OUTLIER) cc_final: 0.9079 (ppp) REVERT: C 369 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9290 (tt) REVERT: C 374 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: C 416 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 422 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8649 (mp10) REVERT: C 475 MET cc_start: 0.8630 (tpp) cc_final: 0.8386 (tpt) REVERT: C 479 TRP cc_start: 0.9470 (m-10) cc_final: 0.8191 (m-10) REVERT: D 579 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: D 626 MET cc_start: 0.9317 (mmm) cc_final: 0.8755 (tpp) REVERT: D 632 ASP cc_start: 0.9722 (t0) cc_final: 0.9505 (m-30) REVERT: E 104 MET cc_start: 0.9596 (OUTLIER) cc_final: 0.9233 (ppp) REVERT: E 161 MET cc_start: 0.8681 (mmm) cc_final: 0.8296 (tmm) REVERT: E 369 LEU cc_start: 0.9529 (tp) cc_final: 0.9153 (tt) REVERT: E 387 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.8798 (p) REVERT: E 475 MET cc_start: 0.9350 (tpp) cc_final: 0.8956 (tpp) REVERT: F 542 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8753 (ttm110) REVERT: F 626 MET cc_start: 0.9003 (tpp) cc_final: 0.8622 (tpp) REVERT: F 627 THR cc_start: 0.9688 (OUTLIER) cc_final: 0.9404 (p) REVERT: H 2 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7564 (t) REVERT: H 3 GLN cc_start: 0.9006 (pm20) cc_final: 0.8295 (pm20) REVERT: H 76 ASN cc_start: 0.8945 (p0) cc_final: 0.8525 (p0) REVERT: H 100 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9116 (t) REVERT: I 3 GLN cc_start: 0.9100 (pm20) cc_final: 0.8596 (pm20) REVERT: I 4 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8026 (tt) REVERT: I 29 LEU cc_start: 0.9273 (mt) cc_final: 0.9053 (mp) REVERT: I 55 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9063 (ttpt) REVERT: J 3 GLN cc_start: 0.9246 (pm20) cc_final: 0.8695 (pm20) REVERT: J 4 LEU cc_start: 0.8920 (mt) cc_final: 0.8492 (tt) REVERT: J 37 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8646 (t80) REVERT: J 76 ASN cc_start: 0.9077 (p0) cc_final: 0.8707 (p0) outliers start: 96 outliers final: 45 residues processed: 248 average time/residue: 0.2871 time to fit residues: 108.2539 Evaluate side-chains 212 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 149 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 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 258 GLN 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 C residue 100 MET Chi-restraints excluded: chain C residue 104 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 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU 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 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 104 MET Chi-restraints excluded: chain E residue 127 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 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU 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 55 LYS Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 100 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 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 183 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 176 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 172 optimal weight: 0.0050 overall best weight: 2.1398 ------------------------------------------------------------------------------- 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** ** C 195 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** F 640 GLN ** I 56 ASN ** 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 = 0.3013 r_free = 0.3013 target = 0.044712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.033015 restraints weight = 96917.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034376 restraints weight = 53498.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.035354 restraints weight = 36689.570| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 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 : 0.003 0.041 17943 Z= 0.158 Angle : 0.730 13.839 24493 Z= 0.362 Chirality : 0.046 0.261 2922 Planarity : 0.004 0.061 3009 Dihedral : 9.193 109.849 3830 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.46 % Favored : 89.10 % Rotamer: Outliers : 4.88 % Allowed : 28.62 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.18), residues: 2065 helix: -0.46 (0.29), residues: 358 sheet: -0.26 (0.24), residues: 481 loop : -2.56 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 623 HIS 0.003 0.001 HIS J 61 PHE 0.042 0.001 PHE J 27 TYR 0.017 0.001 TYR A 61 ARG 0.003 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 49) link_NAG-ASN : angle 2.61900 ( 147) link_BETA1-4 : bond 0.00275 ( 25) link_BETA1-4 : angle 1.29022 ( 75) link_ALPHA1-3 : bond 0.01032 ( 2) link_ALPHA1-3 : angle 2.74847 ( 6) hydrogen bonds : bond 0.03668 ( 419) hydrogen bonds : angle 4.98193 ( 1101) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.58790 ( 84) covalent geometry : bond 0.00349 (17825) covalent geometry : angle 0.69461 (24181) *********************** 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 250 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 161 time to evaluate : 3.106 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 71 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.8899 (t) REVERT: A 95 MET cc_start: 0.9173 (ptm) cc_final: 0.8837 (ptm) REVERT: A 104 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9279 (ptm) REVERT: A 125 LEU cc_start: 0.9684 (tp) cc_final: 0.9454 (mm) REVERT: A 150 MET cc_start: 0.7937 (mtm) cc_final: 0.7609 (mpp) REVERT: A 258 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: A 342 LEU cc_start: 0.9639 (mt) cc_final: 0.9213 (tp) REVERT: A 369 LEU cc_start: 0.9620 (tp) cc_final: 0.9410 (tt) REVERT: A 475 MET cc_start: 0.8980 (tpp) cc_final: 0.8626 (tpt) REVERT: B 535 MET cc_start: 0.9593 (mmt) cc_final: 0.9379 (mmt) REVERT: B 589 ASP cc_start: 0.9074 (m-30) cc_final: 0.8726 (p0) REVERT: B 657 GLU cc_start: 0.9629 (tt0) cc_final: 0.9335 (tm-30) REVERT: C 95 MET cc_start: 0.9219 (ptm) cc_final: 0.7899 (ppp) REVERT: C 121 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9037 (tptp) REVERT: C 190 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8790 (pm20) REVERT: C 369 LEU cc_start: 0.9552 (tt) cc_final: 0.9335 (tt) REVERT: C 374 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7724 (t-90) REVERT: C 416 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8452 (pp) REVERT: C 422 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8669 (mp10) REVERT: C 479 TRP cc_start: 0.9476 (m-10) cc_final: 0.9205 (m-10) REVERT: D 579 ARG cc_start: 0.8274 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: D 626 MET cc_start: 0.9321 (mmm) cc_final: 0.8467 (tpp) REVERT: D 661 LEU cc_start: 0.9614 (tt) cc_final: 0.9394 (pp) REVERT: E 95 MET cc_start: 0.9393 (ppp) cc_final: 0.9186 (ppp) REVERT: E 104 MET cc_start: 0.9659 (OUTLIER) cc_final: 0.9424 (ptm) REVERT: E 161 MET cc_start: 0.8720 (mmm) cc_final: 0.8326 (tmm) REVERT: E 369 LEU cc_start: 0.9610 (tp) cc_final: 0.9267 (tt) REVERT: E 387 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8743 (p) REVERT: F 530 MET cc_start: 0.9023 (tpp) cc_final: 0.8577 (tpp) REVERT: F 542 ARG cc_start: 0.8973 (ttm110) cc_final: 0.8744 (ttm110) REVERT: F 626 MET cc_start: 0.8981 (tpp) cc_final: 0.8549 (tpp) REVERT: F 627 THR cc_start: 0.9661 (OUTLIER) cc_final: 0.9343 (p) REVERT: H 3 GLN cc_start: 0.9023 (pm20) cc_final: 0.8324 (pm20) REVERT: H 4 LEU cc_start: 0.8078 (mt) cc_final: 0.7402 (tp) REVERT: H 76 ASN cc_start: 0.9070 (p0) cc_final: 0.8674 (p0) REVERT: H 100 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.9098 (t) REVERT: I 3 GLN cc_start: 0.9055 (pm20) cc_final: 0.8552 (pm20) REVERT: I 4 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8049 (tt) REVERT: I 55 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9205 (ttpt) REVERT: I 76 ASN cc_start: 0.9088 (m-40) cc_final: 0.8855 (p0) REVERT: J 3 GLN cc_start: 0.9234 (pm20) cc_final: 0.8656 (pm20) REVERT: J 4 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8406 (tt) REVERT: J 37 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8638 (t80) REVERT: J 76 ASN cc_start: 0.9184 (p0) cc_final: 0.8796 (p0) outliers start: 89 outliers final: 49 residues processed: 240 average time/residue: 0.3866 time to fit residues: 145.4193 Evaluate side-chains 209 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 2.041 ------------------------------------------------------------------------------- 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 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 258 GLN 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 B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 190 GLU 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 320 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU 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 630 GLN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 E residue 443 ILE Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 18 LEU 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 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 94 THR 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 197 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 188 ASN ** 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 = 0.2998 r_free = 0.2998 target = 0.043963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.032321 restraints weight = 98910.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.033693 restraints weight = 54310.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.034655 restraints weight = 37008.237| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17943 Z= 0.167 Angle : 0.730 14.130 24493 Z= 0.362 Chirality : 0.045 0.264 2922 Planarity : 0.004 0.060 3009 Dihedral : 8.712 108.920 3830 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.41 % Favored : 89.15 % Rotamer: Outliers : 4.82 % Allowed : 27.91 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.18), residues: 2065 helix: -0.44 (0.28), residues: 361 sheet: -0.42 (0.24), residues: 499 loop : -2.48 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 623 HIS 0.002 0.001 HIS H 61 PHE 0.017 0.001 PHE H 102 TYR 0.011 0.001 TYR E 318 ARG 0.010 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 49) link_NAG-ASN : angle 2.62108 ( 147) link_BETA1-4 : bond 0.00239 ( 25) link_BETA1-4 : angle 1.29341 ( 75) link_ALPHA1-3 : bond 0.00751 ( 2) link_ALPHA1-3 : angle 2.67016 ( 6) hydrogen bonds : bond 0.03611 ( 419) hydrogen bonds : angle 4.87274 ( 1101) SS BOND : bond 0.00353 ( 42) SS BOND : angle 1.61591 ( 84) covalent geometry : bond 0.00367 (17825) covalent geometry : angle 0.69451 (24181) *********************** 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 242 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 154 time to evaluate : 2.006 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: 0.9175 (ptm) cc_final: 0.8836 (ptm) REVERT: A 125 LEU cc_start: 0.9680 (tp) cc_final: 0.9411 (mm) REVERT: A 369 LEU cc_start: 0.9633 (tp) cc_final: 0.9412 (tt) REVERT: A 475 MET cc_start: 0.9034 (tpp) cc_final: 0.8325 (tpp) REVERT: A 478 ASN cc_start: 0.9441 (m110) cc_final: 0.8999 (p0) REVERT: B 535 MET cc_start: 0.9558 (mmt) cc_final: 0.9331 (mmt) REVERT: B 654 GLU cc_start: 0.9616 (tm-30) cc_final: 0.9385 (pp20) REVERT: B 657 GLU cc_start: 0.9629 (tt0) cc_final: 0.9357 (tm-30) REVERT: C 95 MET cc_start: 0.9227 (ptm) cc_final: 0.8433 (tmm) REVERT: C 104 MET cc_start: 0.9690 (ptm) cc_final: 0.9352 (tmm) REVERT: C 121 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9097 (tptp) REVERT: C 161 MET cc_start: 0.9156 (mmm) cc_final: 0.8754 (tmm) REVERT: C 190 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: C 369 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9398 (tt) REVERT: C 374 HIS cc_start: 0.8344 (OUTLIER) cc_final: 0.7783 (t-90) REVERT: C 416 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8492 (pp) REVERT: C 422 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8628 (mp10) REVERT: C 475 MET cc_start: 0.8702 (tpp) cc_final: 0.8321 (tpt) REVERT: D 579 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: D 626 MET cc_start: 0.9328 (mmm) cc_final: 0.8418 (tpp) REVERT: E 95 MET cc_start: 0.9424 (ppp) cc_final: 0.9166 (ppp) REVERT: E 104 MET cc_start: 0.9686 (OUTLIER) cc_final: 0.9221 (ppp) REVERT: E 161 MET cc_start: 0.8781 (mmm) cc_final: 0.8296 (tmm) REVERT: E 369 LEU cc_start: 0.9645 (tp) cc_final: 0.9324 (tt) REVERT: E 387 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8750 (p) REVERT: E 475 MET cc_start: 0.9389 (tpp) cc_final: 0.9064 (tpp) REVERT: F 542 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8763 (ttm110) REVERT: F 626 MET cc_start: 0.8980 (tpp) cc_final: 0.8341 (tpp) REVERT: H 2 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7649 (t) REVERT: H 3 GLN cc_start: 0.8955 (pm20) cc_final: 0.8237 (pm20) REVERT: H 4 LEU cc_start: 0.8106 (mt) cc_final: 0.7410 (tp) REVERT: H 76 ASN cc_start: 0.9120 (p0) cc_final: 0.8701 (p0) REVERT: H 82 MET cc_start: 0.9541 (mmm) cc_final: 0.9314 (mmm) REVERT: H 100 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9050 (t) REVERT: I 3 GLN cc_start: 0.9011 (pm20) cc_final: 0.8711 (pm20) REVERT: I 55 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9330 (ttpt) REVERT: I 76 ASN cc_start: 0.9107 (m-40) cc_final: 0.8883 (p0) REVERT: J 3 GLN cc_start: 0.9206 (pm20) cc_final: 0.8583 (pm20) REVERT: J 4 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8416 (tt) REVERT: J 37 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8637 (t80) REVERT: J 76 ASN cc_start: 0.9198 (p0) cc_final: 0.8754 (p0) outliers start: 88 outliers final: 54 residues processed: 233 average time/residue: 0.3138 time to fit residues: 112.2258 Evaluate side-chains 213 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 146 time to evaluate : 1.922 ------------------------------------------------------------------------------- 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 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 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 190 GLU 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 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU 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 630 GLN Chi-restraints excluded: chain D residue 635 ILE 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 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 660 LEU 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 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 12 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 94 THR 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 168 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 129 optimal weight: 0.0570 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN D 540 GLN D 590 GLN E 188 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.045939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.034270 restraints weight = 95986.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.035649 restraints weight = 52692.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036602 restraints weight = 36083.684| |-----------------------------------------------------------------------------| r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17943 Z= 0.120 Angle : 0.717 14.059 24493 Z= 0.353 Chirality : 0.045 0.252 2922 Planarity : 0.004 0.058 3009 Dihedral : 8.260 107.253 3829 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.78 % Favored : 89.78 % Rotamer: Outliers : 3.95 % Allowed : 28.02 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.19), residues: 2065 helix: -0.30 (0.29), residues: 358 sheet: -0.28 (0.24), residues: 503 loop : -2.41 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 623 HIS 0.003 0.001 HIS C 216 PHE 0.033 0.001 PHE H 27 TYR 0.016 0.001 TYR E 39 ARG 0.012 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.53340 ( 147) link_BETA1-4 : bond 0.00371 ( 25) link_BETA1-4 : angle 1.15068 ( 75) link_ALPHA1-3 : bond 0.00666 ( 2) link_ALPHA1-3 : angle 2.64055 ( 6) hydrogen bonds : bond 0.03257 ( 419) hydrogen bonds : angle 4.69291 ( 1101) SS BOND : bond 0.00336 ( 42) SS BOND : angle 1.39394 ( 84) covalent geometry : bond 0.00272 (17825) covalent geometry : angle 0.68478 (24181) *********************** 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 236 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 164 time to evaluate : 2.139 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: 0.9173 (ptm) cc_final: 0.8806 (ptm) REVERT: A 104 MET cc_start: 0.9375 (ptm) cc_final: 0.8866 (ppp) REVERT: A 325 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 369 LEU cc_start: 0.9646 (tp) cc_final: 0.9404 (tt) REVERT: A 475 MET cc_start: 0.8995 (tpp) cc_final: 0.8354 (tpp) REVERT: A 478 ASN cc_start: 0.9437 (m110) cc_final: 0.9014 (p0) REVERT: B 535 MET cc_start: 0.9569 (mmt) cc_final: 0.9343 (mpp) REVERT: B 589 ASP cc_start: 0.9081 (m-30) cc_final: 0.8806 (p0) REVERT: B 654 GLU cc_start: 0.9706 (tm-30) cc_final: 0.9448 (pp20) REVERT: B 657 GLU cc_start: 0.9598 (tt0) cc_final: 0.9350 (tm-30) REVERT: C 95 MET cc_start: 0.9255 (ptm) cc_final: 0.7953 (ppp) REVERT: C 104 MET cc_start: 0.9669 (ptm) cc_final: 0.9095 (tmm) REVERT: C 190 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8822 (pm20) REVERT: C 194 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9183 (pt) REVERT: C 258 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8766 (pt0) REVERT: C 369 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9381 (tt) REVERT: C 374 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7479 (t-90) REVERT: C 475 MET cc_start: 0.8848 (tpp) cc_final: 0.8252 (tpt) REVERT: C 479 TRP cc_start: 0.9451 (m-10) cc_final: 0.8312 (m-10) REVERT: D 579 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7911 (mtm-85) REVERT: D 626 MET cc_start: 0.9292 (mmm) cc_final: 0.8329 (tpp) REVERT: E 95 MET cc_start: 0.9425 (ppp) cc_final: 0.9131 (ppp) REVERT: E 104 MET cc_start: 0.9691 (OUTLIER) cc_final: 0.9450 (ptm) REVERT: E 150 MET cc_start: 0.8616 (mpp) cc_final: 0.7980 (mpp) REVERT: E 161 MET cc_start: 0.8783 (mmm) cc_final: 0.8156 (tmm) REVERT: E 166 ARG cc_start: 0.8702 (ttp80) cc_final: 0.8475 (ttp80) REVERT: E 369 LEU cc_start: 0.9570 (tp) cc_final: 0.9284 (tt) REVERT: E 387 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.8801 (p) REVERT: E 475 MET cc_start: 0.9401 (tpp) cc_final: 0.9042 (tpp) REVERT: F 542 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8746 (ttm110) REVERT: F 603 ILE cc_start: 0.8922 (pt) cc_final: 0.8633 (pt) REVERT: F 626 MET cc_start: 0.9079 (tpp) cc_final: 0.8294 (tpp) REVERT: H 2 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7496 (t) REVERT: H 3 GLN cc_start: 0.8965 (pm20) cc_final: 0.8269 (pm20) REVERT: H 4 LEU cc_start: 0.8050 (mt) cc_final: 0.7570 (mt) REVERT: H 76 ASN cc_start: 0.9136 (p0) cc_final: 0.8683 (p0) REVERT: H 97 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7759 (tpp80) REVERT: H 100 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8998 (t) REVERT: I 3 GLN cc_start: 0.9137 (pm20) cc_final: 0.8533 (pm20) REVERT: I 4 LEU cc_start: 0.9291 (mm) cc_final: 0.8740 (mt) REVERT: I 55 LYS cc_start: 0.9547 (ttpt) cc_final: 0.9312 (ttpt) REVERT: I 76 ASN cc_start: 0.9120 (m-40) cc_final: 0.8866 (p0) REVERT: J 3 GLN cc_start: 0.9230 (pm20) cc_final: 0.8603 (pm20) REVERT: J 4 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8321 (tt) REVERT: J 37 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8583 (t80) REVERT: J 76 ASN cc_start: 0.9180 (p0) cc_final: 0.8673 (p0) REVERT: J 87 THR cc_start: 0.9153 (OUTLIER) cc_final: 0.8789 (m) outliers start: 72 outliers final: 44 residues processed: 228 average time/residue: 0.4924 time to fit residues: 176.7866 Evaluate side-chains 212 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 155 time to evaluate : 5.655 ------------------------------------------------------------------------------- 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 126 CYS 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 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 325 ASP 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 127 VAL Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 205 CYS 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 369 LEU Chi-restraints excluded: chain C residue 374 HIS 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 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 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU 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 100 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 87 THR 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 140 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** E 258 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.043192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.031514 restraints weight = 100779.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.032833 restraints weight = 56084.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.033761 restraints weight = 38776.767| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17943 Z= 0.227 Angle : 0.779 16.864 24493 Z= 0.378 Chirality : 0.045 0.277 2922 Planarity : 0.004 0.058 3009 Dihedral : 8.232 107.233 3828 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.46 % Favored : 89.15 % Rotamer: Outliers : 4.06 % Allowed : 28.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2065 helix: 0.07 (0.29), residues: 331 sheet: -0.18 (0.25), residues: 439 loop : -2.37 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 623 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.001 PHE H 102 TYR 0.011 0.001 TYR E 39 ARG 0.010 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 49) link_NAG-ASN : angle 2.64580 ( 147) link_BETA1-4 : bond 0.00168 ( 25) link_BETA1-4 : angle 1.41435 ( 75) link_ALPHA1-3 : bond 0.00563 ( 2) link_ALPHA1-3 : angle 2.44946 ( 6) hydrogen bonds : bond 0.03742 ( 419) hydrogen bonds : angle 4.86817 ( 1101) SS BOND : bond 0.00392 ( 42) SS BOND : angle 1.59881 ( 84) covalent geometry : bond 0.00489 (17825) covalent geometry : angle 0.74580 (24181) *********************** 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 219 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 145 time to evaluate : 2.087 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 95 MET cc_start: 0.9227 (ptm) cc_final: 0.8875 (ptm) REVERT: A 104 MET cc_start: 0.9397 (ptm) cc_final: 0.8814 (ppp) REVERT: A 258 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8536 (pt0) REVERT: A 325 ASP cc_start: 0.9099 (OUTLIER) cc_final: 0.8522 (t0) REVERT: A 475 MET cc_start: 0.9014 (tpp) cc_final: 0.8444 (tpp) REVERT: A 478 ASN cc_start: 0.9371 (m110) cc_final: 0.8951 (p0) REVERT: B 535 MET cc_start: 0.9573 (mmt) cc_final: 0.9363 (mmt) REVERT: B 589 ASP cc_start: 0.9140 (m-30) cc_final: 0.8869 (p0) REVERT: B 657 GLU cc_start: 0.9621 (tt0) cc_final: 0.9388 (tm-30) REVERT: C 95 MET cc_start: 0.9246 (ptm) cc_final: 0.8492 (tmm) REVERT: C 104 MET cc_start: 0.9688 (ptm) cc_final: 0.9355 (tmm) REVERT: C 190 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: C 258 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8742 (pt0) REVERT: C 374 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.7966 (t-90) REVERT: C 422 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8638 (mp10) REVERT: C 475 MET cc_start: 0.8843 (tpp) cc_final: 0.8487 (tpt) REVERT: D 579 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: D 626 MET cc_start: 0.9209 (mmm) cc_final: 0.8239 (tpp) REVERT: E 95 MET cc_start: 0.9492 (ppp) cc_final: 0.9199 (ppp) REVERT: E 104 MET cc_start: 0.9704 (OUTLIER) cc_final: 0.9247 (ppp) REVERT: E 150 MET cc_start: 0.8708 (mpp) cc_final: 0.8095 (mpp) REVERT: E 161 MET cc_start: 0.8881 (mmm) cc_final: 0.8630 (tpp) REVERT: E 369 LEU cc_start: 0.9607 (tp) cc_final: 0.9348 (tt) REVERT: E 387 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8779 (p) REVERT: E 475 MET cc_start: 0.9379 (tpp) cc_final: 0.9094 (tpp) REVERT: F 542 ARG cc_start: 0.9133 (ttm110) cc_final: 0.8891 (ttm110) REVERT: F 626 MET cc_start: 0.8953 (tpp) cc_final: 0.8296 (tpp) REVERT: H 2 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7592 (t) REVERT: H 3 GLN cc_start: 0.9021 (pm20) cc_final: 0.8385 (pm20) REVERT: H 4 LEU cc_start: 0.8127 (mt) cc_final: 0.7652 (mt) REVERT: H 76 ASN cc_start: 0.9158 (p0) cc_final: 0.8721 (p0) REVERT: H 100 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9025 (t) REVERT: I 3 GLN cc_start: 0.9241 (pm20) cc_final: 0.8660 (pm20) REVERT: I 4 LEU cc_start: 0.9246 (mm) cc_final: 0.8687 (mt) REVERT: J 3 GLN cc_start: 0.9273 (pm20) cc_final: 0.8877 (pm20) REVERT: J 4 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8339 (tt) REVERT: J 37 PHE cc_start: 0.9040 (OUTLIER) cc_final: 0.8594 (t80) REVERT: J 76 ASN cc_start: 0.9215 (p0) cc_final: 0.8720 (p0) REVERT: J 87 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8828 (m) outliers start: 74 outliers final: 47 residues processed: 208 average time/residue: 0.2861 time to fit residues: 91.1501 Evaluate side-chains 199 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 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 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 491 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 190 GLU 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 374 HIS 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 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 571 TRP 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 48 VAL 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 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 87 THR 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 155 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 203 optimal weight: 30.0000 chunk 85 optimal weight: 0.0970 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN B 651 ASN ** D 540 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.045130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.033428 restraints weight = 98323.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.034734 restraints weight = 55029.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035671 restraints weight = 38206.951| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17943 Z= 0.137 Angle : 0.758 14.249 24493 Z= 0.366 Chirality : 0.045 0.266 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.983 106.025 3828 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.98 % Favored : 89.64 % Rotamer: Outliers : 3.51 % Allowed : 29.28 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.19), residues: 2065 helix: 0.12 (0.30), residues: 328 sheet: -0.27 (0.24), residues: 503 loop : -2.35 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS C 216 PHE 0.028 0.001 PHE J 27 TYR 0.040 0.001 TYR C 61 ARG 0.013 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 49) link_NAG-ASN : angle 2.52980 ( 147) link_BETA1-4 : bond 0.00297 ( 25) link_BETA1-4 : angle 1.15571 ( 75) link_ALPHA1-3 : bond 0.00685 ( 2) link_ALPHA1-3 : angle 2.54870 ( 6) hydrogen bonds : bond 0.03413 ( 419) hydrogen bonds : angle 4.67276 ( 1101) SS BOND : bond 0.00312 ( 42) SS BOND : angle 2.05226 ( 84) covalent geometry : bond 0.00312 (17825) covalent geometry : angle 0.72246 (24181) *********************** 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 213 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 149 time to evaluate : 2.015 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: 0.9176 (ptm) cc_final: 0.8799 (ptm) REVERT: A 104 MET cc_start: 0.9429 (ptm) cc_final: 0.8831 (ppp) REVERT: A 258 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8140 (pt0) REVERT: A 475 MET cc_start: 0.8973 (tpp) cc_final: 0.8428 (tpp) REVERT: A 478 ASN cc_start: 0.9357 (m110) cc_final: 0.8933 (p0) REVERT: B 589 ASP cc_start: 0.9122 (m-30) cc_final: 0.8810 (p0) REVERT: B 657 GLU cc_start: 0.9648 (tt0) cc_final: 0.9423 (tm-30) REVERT: C 95 MET cc_start: 0.9256 (ptm) cc_final: 0.8511 (tmm) REVERT: C 104 MET cc_start: 0.9688 (ptm) cc_final: 0.9368 (tmm) REVERT: C 190 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: C 258 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8753 (pt0) REVERT: C 374 HIS cc_start: 0.8347 (OUTLIER) cc_final: 0.7730 (t-90) REVERT: C 475 MET cc_start: 0.8806 (tpp) cc_final: 0.8419 (tpt) REVERT: D 579 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: D 589 ASP cc_start: 0.9165 (m-30) cc_final: 0.8773 (p0) REVERT: D 626 MET cc_start: 0.9264 (mmm) cc_final: 0.8426 (tpp) REVERT: E 95 MET cc_start: 0.9492 (ppp) cc_final: 0.9176 (ppp) REVERT: E 104 MET cc_start: 0.9708 (OUTLIER) cc_final: 0.9270 (ppp) REVERT: E 150 MET cc_start: 0.8687 (mpp) cc_final: 0.8061 (mpp) REVERT: E 161 MET cc_start: 0.8861 (mmm) cc_final: 0.8586 (tpp) REVERT: E 166 ARG cc_start: 0.8750 (ttp80) cc_final: 0.8517 (ttp80) REVERT: E 369 LEU cc_start: 0.9593 (tp) cc_final: 0.9366 (tt) REVERT: E 387 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8789 (p) REVERT: E 475 MET cc_start: 0.9419 (tpp) cc_final: 0.9127 (tpp) REVERT: F 542 ARG cc_start: 0.9134 (ttm110) cc_final: 0.8879 (ttm110) REVERT: F 589 ASP cc_start: 0.9155 (m-30) cc_final: 0.8657 (p0) REVERT: F 593 LEU cc_start: 0.8813 (pp) cc_final: 0.8541 (pp) REVERT: F 626 MET cc_start: 0.9100 (tpp) cc_final: 0.8604 (tpp) REVERT: H 2 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7609 (t) REVERT: H 3 GLN cc_start: 0.8997 (pm20) cc_final: 0.8411 (pm20) REVERT: H 4 LEU cc_start: 0.8200 (mt) cc_final: 0.7722 (mt) REVERT: H 76 ASN cc_start: 0.9150 (p0) cc_final: 0.8693 (p0) REVERT: H 100 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8970 (t) REVERT: I 3 GLN cc_start: 0.9201 (pm20) cc_final: 0.8617 (pm20) REVERT: I 4 LEU cc_start: 0.9231 (mm) cc_final: 0.8736 (mt) REVERT: I 76 ASN cc_start: 0.9150 (m-40) cc_final: 0.8887 (p0) REVERT: J 3 GLN cc_start: 0.9258 (pm20) cc_final: 0.8794 (pm20) REVERT: J 4 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8449 (tt) REVERT: J 37 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8769 (t80) REVERT: J 45 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.7881 (ptt90) REVERT: J 76 ASN cc_start: 0.9224 (p0) cc_final: 0.8698 (p0) REVERT: J 87 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8811 (m) outliers start: 64 outliers final: 42 residues processed: 207 average time/residue: 0.2880 time to fit residues: 91.3547 Evaluate side-chains 199 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 1.905 ------------------------------------------------------------------------------- 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 126 CYS Chi-restraints excluded: chain A residue 194 ILE 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 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 190 GLU 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 374 HIS Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL 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 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 45 ARG Chi-restraints excluded: chain J residue 87 THR 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 66 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 157 optimal weight: 0.5980 chunk 44 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 95 optimal weight: 0.0270 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 128 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 575 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 = 0.3015 r_free = 0.3015 target = 0.044609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.032952 restraints weight = 99137.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034330 restraints weight = 54667.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035313 restraints weight = 37238.694| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17943 Z= 0.120 Angle : 0.774 16.136 24493 Z= 0.369 Chirality : 0.046 0.250 2922 Planarity : 0.004 0.063 3009 Dihedral : 7.757 104.815 3828 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.69 % Favored : 89.93 % Rotamer: Outliers : 3.07 % Allowed : 29.33 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.19), residues: 2065 helix: 0.38 (0.31), residues: 319 sheet: -0.29 (0.23), residues: 521 loop : -2.29 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS C 216 PHE 0.010 0.001 PHE C 233 TYR 0.012 0.001 TYR E 318 ARG 0.014 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 49) link_NAG-ASN : angle 2.48666 ( 147) link_BETA1-4 : bond 0.00368 ( 25) link_BETA1-4 : angle 1.11440 ( 75) link_ALPHA1-3 : bond 0.00836 ( 2) link_ALPHA1-3 : angle 2.55878 ( 6) hydrogen bonds : bond 0.03211 ( 419) hydrogen bonds : angle 4.60778 ( 1101) SS BOND : bond 0.00321 ( 42) SS BOND : angle 1.73702 ( 84) covalent geometry : bond 0.00274 (17825) covalent geometry : angle 0.74410 (24181) *********************** 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 212 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 156 time to evaluate : 2.359 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 95 MET cc_start: 0.9193 (ptm) cc_final: 0.8790 (ptm) REVERT: A 104 MET cc_start: 0.9416 (ptm) cc_final: 0.8922 (ppp) REVERT: A 258 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8256 (pt0) REVERT: A 475 MET cc_start: 0.8992 (tpp) cc_final: 0.8492 (tpp) REVERT: A 478 ASN cc_start: 0.9369 (m110) cc_final: 0.8943 (p0) REVERT: B 544 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9210 (mm) REVERT: B 589 ASP cc_start: 0.9102 (m-30) cc_final: 0.8802 (p0) REVERT: B 657 GLU cc_start: 0.9655 (tt0) cc_final: 0.9403 (tm-30) REVERT: C 95 MET cc_start: 0.9298 (ptm) cc_final: 0.8521 (tmm) REVERT: C 104 MET cc_start: 0.9685 (ptm) cc_final: 0.9104 (tmm) REVERT: C 121 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9109 (tptp) REVERT: C 190 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8834 (pm20) REVERT: C 258 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8687 (pt0) REVERT: C 374 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7543 (t-90) REVERT: C 475 MET cc_start: 0.8821 (tpp) cc_final: 0.8364 (tpt) REVERT: C 479 TRP cc_start: 0.9422 (m-10) cc_final: 0.8335 (m-10) REVERT: D 542 ARG cc_start: 0.8965 (ttm110) cc_final: 0.8738 (ttp-110) REVERT: D 579 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.7892 (mtm-85) REVERT: D 589 ASP cc_start: 0.9162 (m-30) cc_final: 0.8764 (p0) REVERT: D 626 MET cc_start: 0.9271 (mmm) cc_final: 0.8370 (tpp) REVERT: E 95 MET cc_start: 0.9467 (ppp) cc_final: 0.9131 (ppp) REVERT: E 104 MET cc_start: 0.9710 (OUTLIER) cc_final: 0.9475 (ptm) REVERT: E 150 MET cc_start: 0.8658 (mpp) cc_final: 0.8045 (mpp) REVERT: E 161 MET cc_start: 0.8899 (mmm) cc_final: 0.8614 (tpp) REVERT: E 166 ARG cc_start: 0.8725 (ttp80) cc_final: 0.8479 (ttp80) REVERT: E 369 LEU cc_start: 0.9576 (tp) cc_final: 0.9362 (tt) REVERT: F 542 ARG cc_start: 0.9113 (ttm110) cc_final: 0.8847 (ttm110) REVERT: F 579 ARG cc_start: 0.8351 (mtm-85) cc_final: 0.7718 (mtm-85) REVERT: F 589 ASP cc_start: 0.9138 (m-30) cc_final: 0.8643 (p0) REVERT: F 626 MET cc_start: 0.9028 (tpp) cc_final: 0.8299 (tpp) REVERT: H 2 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7578 (t) REVERT: H 3 GLN cc_start: 0.8987 (pm20) cc_final: 0.8383 (pm20) REVERT: H 4 LEU cc_start: 0.8119 (mt) cc_final: 0.7611 (mt) REVERT: H 76 ASN cc_start: 0.9159 (p0) cc_final: 0.8713 (p0) REVERT: H 97 ARG cc_start: 0.8466 (tpp80) cc_final: 0.7817 (tpp80) REVERT: H 100 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.8930 (t) REVERT: I 3 GLN cc_start: 0.9155 (pm20) cc_final: 0.8671 (pm20) REVERT: I 76 ASN cc_start: 0.9134 (m-40) cc_final: 0.8879 (p0) REVERT: J 3 GLN cc_start: 0.9235 (pm20) cc_final: 0.8758 (pm20) REVERT: J 4 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8353 (tt) REVERT: J 37 PHE cc_start: 0.8945 (OUTLIER) cc_final: 0.8540 (t80) REVERT: J 64 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8948 (mmmm) REVERT: J 76 ASN cc_start: 0.9209 (p0) cc_final: 0.8651 (p0) REVERT: J 87 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8696 (m) outliers start: 56 outliers final: 40 residues processed: 204 average time/residue: 0.3314 time to fit residues: 104.2078 Evaluate side-chains 199 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 147 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 126 CYS 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 424 ILE Chi-restraints excluded: chain B residue 544 LEU 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 190 GLU 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 374 HIS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 104 MET 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 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 2 VAL 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 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 193 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 258 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.032723 restraints weight = 100505.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.034009 restraints weight = 56539.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.034934 restraints weight = 39106.600| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17943 Z= 0.200 Angle : 0.802 14.187 24493 Z= 0.383 Chirality : 0.045 0.268 2922 Planarity : 0.004 0.058 3009 Dihedral : 7.835 104.378 3828 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.94 % Favored : 88.67 % Rotamer: Outliers : 3.18 % Allowed : 29.61 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 2065 helix: 0.28 (0.30), residues: 328 sheet: -0.23 (0.25), residues: 436 loop : -2.34 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 571 HIS 0.004 0.001 HIS C 216 PHE 0.031 0.002 PHE J 27 TYR 0.013 0.001 TYR H 100B ARG 0.015 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 49) link_NAG-ASN : angle 2.57665 ( 147) link_BETA1-4 : bond 0.00169 ( 25) link_BETA1-4 : angle 1.30960 ( 75) link_ALPHA1-3 : bond 0.00613 ( 2) link_ALPHA1-3 : angle 2.38010 ( 6) hydrogen bonds : bond 0.03547 ( 419) hydrogen bonds : angle 4.74119 ( 1101) SS BOND : bond 0.00302 ( 42) SS BOND : angle 1.89039 ( 84) covalent geometry : bond 0.00438 (17825) covalent geometry : angle 0.76986 (24181) ********************** 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 204 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 2.268 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: A 61 TYR cc_start: 0.8073 (t80) cc_final: 0.7865 (t80) REVERT: A 95 MET cc_start: 0.9216 (ptm) cc_final: 0.8841 (ptm) REVERT: A 104 MET cc_start: 0.9427 (ptm) cc_final: 0.8842 (ppp) REVERT: A 258 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: A 475 MET cc_start: 0.8988 (tpp) cc_final: 0.8458 (tpp) REVERT: A 478 ASN cc_start: 0.9314 (m110) cc_final: 0.8839 (p0) REVERT: B 589 ASP cc_start: 0.9154 (m-30) cc_final: 0.8852 (p0) REVERT: B 657 GLU cc_start: 0.9656 (tt0) cc_final: 0.9416 (tm-30) REVERT: C 95 MET cc_start: 0.9281 (ptm) cc_final: 0.8562 (tmm) REVERT: C 104 MET cc_start: 0.9688 (ptm) cc_final: 0.9113 (ppp) REVERT: C 121 LYS cc_start: 0.9418 (OUTLIER) cc_final: 0.9125 (tptp) REVERT: C 190 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8909 (pm20) REVERT: C 258 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8629 (pt0) REVERT: C 374 HIS cc_start: 0.8509 (OUTLIER) cc_final: 0.7897 (t-90) REVERT: C 475 MET cc_start: 0.8834 (tpp) cc_final: 0.8452 (tpt) REVERT: D 542 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8793 (ttp-110) REVERT: D 589 ASP cc_start: 0.9142 (m-30) cc_final: 0.8763 (p0) REVERT: D 626 MET cc_start: 0.9223 (mmm) cc_final: 0.8374 (tpp) REVERT: E 95 MET cc_start: 0.9502 (ppp) cc_final: 0.9183 (ppp) REVERT: E 104 MET cc_start: 0.9703 (OUTLIER) cc_final: 0.9277 (ppp) REVERT: E 150 MET cc_start: 0.8707 (mpp) cc_final: 0.8117 (mpp) REVERT: E 161 MET cc_start: 0.8901 (mmm) cc_final: 0.8593 (tpp) REVERT: E 166 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8531 (ttp80) REVERT: E 369 LEU cc_start: 0.9582 (tp) cc_final: 0.9377 (tt) REVERT: E 387 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8801 (p) REVERT: E 475 MET cc_start: 0.9330 (tpp) cc_final: 0.8911 (tpp) REVERT: F 542 ARG cc_start: 0.9165 (ttm110) cc_final: 0.8927 (ttm110) REVERT: F 579 ARG cc_start: 0.8368 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: F 589 ASP cc_start: 0.9117 (m-30) cc_final: 0.8670 (p0) REVERT: F 626 MET cc_start: 0.9021 (tpp) cc_final: 0.8309 (tpp) REVERT: H 2 VAL cc_start: 0.8141 (OUTLIER) cc_final: 0.7615 (t) REVERT: H 3 GLN cc_start: 0.9030 (pm20) cc_final: 0.8436 (pm20) REVERT: H 4 LEU cc_start: 0.8228 (mt) cc_final: 0.7748 (mt) REVERT: H 76 ASN cc_start: 0.9162 (p0) cc_final: 0.8697 (p0) REVERT: I 3 GLN cc_start: 0.9156 (pm20) cc_final: 0.8665 (pm20) REVERT: J 3 GLN cc_start: 0.9250 (pm20) cc_final: 0.8850 (pm20) REVERT: J 4 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8327 (tt) REVERT: J 37 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8720 (t80) REVERT: J 45 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8045 (ptt90) REVERT: J 76 ASN cc_start: 0.9216 (p0) cc_final: 0.8687 (p0) REVERT: J 87 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8706 (m) outliers start: 58 outliers final: 42 residues processed: 197 average time/residue: 0.3654 time to fit residues: 111.2048 Evaluate side-chains 199 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 2.307 ------------------------------------------------------------------------------- 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 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 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 190 GLU 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 374 HIS Chi-restraints excluded: chain C residue 488 VAL 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 104 MET Chi-restraints excluded: chain E residue 120 VAL 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 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 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain I residue 2 VAL 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 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 70 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 184 optimal weight: 0.0060 chunk 191 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 85 optimal weight: 0.0040 chunk 45 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** F 575 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 = 0.3015 r_free = 0.3015 target = 0.044540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.032806 restraints weight = 97705.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034182 restraints weight = 53380.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035181 restraints weight = 36255.776| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17943 Z= 0.121 Angle : 0.784 14.271 24493 Z= 0.373 Chirality : 0.046 0.282 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.560 102.690 3828 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.49 % Favored : 90.12 % Rotamer: Outliers : 2.80 % Allowed : 29.77 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.19), residues: 2065 helix: 0.47 (0.31), residues: 319 sheet: -0.23 (0.24), residues: 506 loop : -2.29 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 35 HIS 0.003 0.001 HIS C 216 PHE 0.010 0.001 PHE C 233 TYR 0.013 0.001 TYR E 318 ARG 0.014 0.001 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 49) link_NAG-ASN : angle 2.45218 ( 147) link_BETA1-4 : bond 0.00402 ( 25) link_BETA1-4 : angle 1.06084 ( 75) link_ALPHA1-3 : bond 0.00648 ( 2) link_ALPHA1-3 : angle 2.55578 ( 6) hydrogen bonds : bond 0.03174 ( 419) hydrogen bonds : angle 4.54292 ( 1101) SS BOND : bond 0.00398 ( 42) SS BOND : angle 1.72322 ( 84) covalent geometry : bond 0.00276 (17825) covalent geometry : angle 0.75510 (24181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5860.64 seconds wall clock time: 106 minutes 8.94 seconds (6368.94 seconds total)