Starting phenix.real_space_refine on Sun May 18 20:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tng_41415/05_2025/8tng_41415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tng_41415/05_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_41415/05_2025/8tng_41415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tng_41415/05_2025/8tng_41415.map" model { file = "/net/cci-nas-00/data/ceres_data/8tng_41415/05_2025/8tng_41415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tng_41415/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.85, per 1000 atoms: 0.56 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: 4.53 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: 2.34 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: 5.36 Time building geometry restraints manager: 5.26 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.630 Find NCS groups from input model: 1.080 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.610 ------------------------------------------------------------------------------- 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 : 1.757 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: 0.3273 time to fit residues: 145.9854 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 : 1.817 ------------------------------------------------------------------------------- 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: 0.6980 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: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 188 ASN B 540 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 66 HIS ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.047792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.035531 restraints weight = 96124.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.036976 restraints weight = 51569.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.038017 restraints weight = 35187.395| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17943 Z= 0.202 Angle : 0.820 12.966 24493 Z= 0.410 Chirality : 0.048 0.390 2922 Planarity : 0.004 0.064 3009 Dihedral : 11.425 115.293 3832 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.28 % Favored : 88.23 % Rotamer: Outliers : 6.03 % Allowed : 28.73 % Favored : 65.24 % 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: -2.47 (0.18), residues: 2065 helix: -0.61 (0.29), residues: 344 sheet: -0.38 (0.25), residues: 486 loop : -2.63 (0.17), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 69 HIS 0.004 0.001 HIS H 61 PHE 0.019 0.001 PHE E 382 TYR 0.012 0.001 TYR D 638 ARG 0.008 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00444 ( 49) link_NAG-ASN : angle 2.98572 ( 147) link_BETA1-4 : bond 0.00427 ( 25) link_BETA1-4 : angle 1.43578 ( 75) link_ALPHA1-3 : bond 0.01213 ( 2) link_ALPHA1-3 : angle 2.85220 ( 6) hydrogen bonds : bond 0.04407 ( 419) hydrogen bonds : angle 5.45802 ( 1101) SS BOND : bond 0.00498 ( 42) SS BOND : angle 1.73964 ( 84) covalent geometry : bond 0.00445 (17825) covalent geometry : angle 0.78005 (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 296 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 186 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8956 (m-90) cc_final: 0.8471 (m-90) REVERT: A 95 MET cc_start: 0.9120 (ptm) cc_final: 0.8872 (ptm) REVERT: A 104 MET cc_start: 0.9574 (OUTLIER) cc_final: 0.9057 (ptm) REVERT: A 278 THR cc_start: 0.9661 (OUTLIER) cc_final: 0.9401 (p) REVERT: A 325 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8429 (t0) REVERT: A 326 ILE cc_start: 0.9659 (OUTLIER) cc_final: 0.9432 (mm) REVERT: A 368 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8273 (t0) REVERT: A 370 GLU cc_start: 0.8489 (mp0) cc_final: 0.7468 (mp0) REVERT: B 657 GLU cc_start: 0.9639 (tt0) cc_final: 0.9326 (tm-30) REVERT: C 104 MET cc_start: 0.9605 (OUTLIER) cc_final: 0.9044 (ppp) REVERT: C 302 ASN cc_start: 0.9226 (OUTLIER) cc_final: 0.9002 (m110) REVERT: C 374 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7667 (t-90) REVERT: C 479 TRP cc_start: 0.9275 (m-10) cc_final: 0.8131 (m-10) REVERT: D 579 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.8017 (mtm-85) REVERT: D 626 MET cc_start: 0.9277 (mmm) cc_final: 0.8966 (tpp) REVERT: E 95 MET cc_start: 0.9351 (ppp) cc_final: 0.8870 (ppp) REVERT: E 104 MET cc_start: 0.9554 (OUTLIER) cc_final: 0.9301 (ptm) REVERT: E 296 CYS cc_start: 0.5695 (OUTLIER) cc_final: 0.5455 (m) REVERT: E 443 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9267 (tt) REVERT: E 475 MET cc_start: 0.9238 (tpp) cc_final: 0.8980 (tpp) REVERT: F 589 ASP cc_start: 0.9121 (m-30) cc_final: 0.8680 (p0) REVERT: F 626 MET cc_start: 0.9224 (tpp) cc_final: 0.8742 (tpt) REVERT: F 627 THR cc_start: 0.9800 (OUTLIER) cc_final: 0.9521 (p) REVERT: H 3 GLN cc_start: 0.9103 (pm20) cc_final: 0.8448 (pm20) REVERT: H 19 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.9159 (tpt90) REVERT: H 76 ASN cc_start: 0.8865 (p0) cc_final: 0.8560 (p0) REVERT: H 100 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8459 (t0) REVERT: H 100 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9112 (t) REVERT: I 3 GLN cc_start: 0.9101 (pm20) cc_final: 0.8711 (pm20) REVERT: I 76 ASN cc_start: 0.8929 (p0) cc_final: 0.8621 (p0) REVERT: J 3 GLN cc_start: 0.9302 (pm20) cc_final: 0.8848 (pm20) REVERT: J 37 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8701 (t80) REVERT: J 76 ASN cc_start: 0.8930 (p0) cc_final: 0.8681 (p0) outliers start: 110 outliers final: 40 residues processed: 281 average time/residue: 0.2835 time to fit residues: 121.3921 Evaluate side-chains 213 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 157 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 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 302 ASN Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 59 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 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 E residue 443 ILE 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 89 VAL 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: 4.9990 chunk 29 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** 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** ** J 5 GLN ** 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 = 0.2997 r_free = 0.2997 target = 0.045077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.033132 restraints weight = 97663.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.034511 restraints weight = 52880.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.035495 restraints weight = 36049.242| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17943 Z= 0.252 Angle : 0.804 13.757 24493 Z= 0.399 Chirality : 0.046 0.274 2922 Planarity : 0.004 0.063 3009 Dihedral : 10.202 112.450 3831 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.90 % Favored : 88.57 % Rotamer: Outliers : 5.43 % Allowed : 29.44 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -2.43 (0.18), residues: 2065 helix: -0.40 (0.29), residues: 333 sheet: -0.52 (0.25), residues: 463 loop : -2.53 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 628 HIS 0.004 0.001 HIS H 61 PHE 0.033 0.002 PHE H 27 TYR 0.011 0.001 TYR A 384 ARG 0.006 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 49) link_NAG-ASN : angle 2.76583 ( 147) link_BETA1-4 : bond 0.00196 ( 25) link_BETA1-4 : angle 1.46664 ( 75) link_ALPHA1-3 : bond 0.00817 ( 2) link_ALPHA1-3 : angle 2.55200 ( 6) hydrogen bonds : bond 0.04207 ( 419) hydrogen bonds : angle 5.28730 ( 1101) SS BOND : bond 0.00552 ( 42) SS BOND : angle 1.68744 ( 84) covalent geometry : bond 0.00538 (17825) covalent geometry : angle 0.76764 (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 263 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 164 time to evaluate : 1.820 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: 0.9118 (ptm) cc_final: 0.8799 (ptm) REVERT: A 104 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9250 (ptm) REVERT: A 125 LEU cc_start: 0.9728 (tp) cc_final: 0.9471 (mm) REVERT: A 150 MET cc_start: 0.8112 (mtm) cc_final: 0.7648 (mpp) REVERT: A 278 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9236 (p) REVERT: A 325 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8459 (t0) REVERT: A 369 LEU cc_start: 0.9568 (tp) cc_final: 0.9317 (tt) REVERT: B 589 ASP cc_start: 0.9028 (m-30) cc_final: 0.8696 (p0) REVERT: B 657 GLU cc_start: 0.9627 (tt0) cc_final: 0.9338 (tm-30) REVERT: C 104 MET cc_start: 0.9637 (OUTLIER) cc_final: 0.9154 (ppp) REVERT: C 252 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9408 (mmmt) REVERT: C 369 LEU cc_start: 0.9557 (tt) cc_final: 0.9308 (tt) REVERT: C 374 HIS cc_start: 0.8426 (OUTLIER) cc_final: 0.8016 (t-90) REVERT: C 416 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8500 (pp) REVERT: C 422 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: C 475 MET cc_start: 0.8678 (tpp) cc_final: 0.8447 (tpt) REVERT: C 479 TRP cc_start: 0.9482 (m-10) cc_final: 0.8345 (m-10) REVERT: D 579 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: D 626 MET cc_start: 0.9319 (mmm) cc_final: 0.8789 (tpp) REVERT: D 632 ASP cc_start: 0.9724 (t0) cc_final: 0.9511 (m-30) REVERT: E 104 MET cc_start: 0.9593 (OUTLIER) cc_final: 0.9217 (ppp) REVERT: E 161 MET cc_start: 0.8622 (mmm) cc_final: 0.8259 (tmm) REVERT: E 369 LEU cc_start: 0.9500 (tp) cc_final: 0.9138 (tt) REVERT: E 387 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.8766 (p) REVERT: E 475 MET cc_start: 0.9344 (tpp) cc_final: 0.8945 (tpp) REVERT: F 542 ARG cc_start: 0.8941 (ttm110) cc_final: 0.7853 (ptp-110) REVERT: F 626 MET cc_start: 0.9042 (tpp) cc_final: 0.8287 (tpp) REVERT: F 657 GLU cc_start: 0.9450 (tt0) cc_final: 0.9012 (pt0) REVERT: H 2 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7656 (t) REVERT: H 3 GLN cc_start: 0.9015 (pm20) cc_final: 0.8313 (pm20) REVERT: H 76 ASN cc_start: 0.8947 (p0) cc_final: 0.8530 (p0) REVERT: H 100 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9134 (t) REVERT: I 3 GLN cc_start: 0.9096 (pm20) cc_final: 0.8603 (pm20) REVERT: I 4 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8097 (tt) REVERT: I 55 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9215 (ttpt) REVERT: J 3 GLN cc_start: 0.9242 (pm20) cc_final: 0.8721 (pm20) REVERT: J 37 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8667 (t80) REVERT: J 76 ASN cc_start: 0.9084 (p0) cc_final: 0.8715 (p0) outliers start: 99 outliers final: 46 residues processed: 251 average time/residue: 0.2818 time to fit residues: 107.9830 Evaluate side-chains 204 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 143 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 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 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 116 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 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 72 HIS Chi-restraints excluded: chain E residue 89 VAL 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 385 CYS 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 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 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: 0.9990 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 68 optimal weight: 0.0170 chunk 176 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 172 optimal weight: 0.0170 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 428 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 540 GLN D 653 GLN E 94 ASN E 188 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.046055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034371 restraints weight = 94771.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.035796 restraints weight = 50872.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.036805 restraints weight = 34385.091| |-----------------------------------------------------------------------------| r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17943 Z= 0.127 Angle : 0.751 13.619 24493 Z= 0.371 Chirality : 0.047 0.266 2922 Planarity : 0.004 0.059 3009 Dihedral : 9.100 108.840 3830 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.93 % Favored : 89.64 % Rotamer: Outliers : 4.17 % Allowed : 28.34 % Favored : 67.49 % 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: -2.28 (0.18), residues: 2065 helix: -0.60 (0.29), residues: 361 sheet: -0.18 (0.24), residues: 485 loop : -2.51 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 35 HIS 0.004 0.001 HIS E 216 PHE 0.015 0.001 PHE J 27 TYR 0.019 0.001 TYR A 61 ARG 0.005 0.000 ARG D 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 49) link_NAG-ASN : angle 2.57504 ( 147) link_BETA1-4 : bond 0.00469 ( 25) link_BETA1-4 : angle 1.17502 ( 75) link_ALPHA1-3 : bond 0.00822 ( 2) link_ALPHA1-3 : angle 2.85522 ( 6) hydrogen bonds : bond 0.03462 ( 419) hydrogen bonds : angle 4.91259 ( 1101) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.54451 ( 84) covalent geometry : bond 0.00283 (17825) covalent geometry : angle 0.71835 (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 254 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 178 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9138 (ptm) cc_final: 0.8776 (ptm) REVERT: A 125 LEU cc_start: 0.9656 (tp) cc_final: 0.9436 (mm) REVERT: A 258 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8442 (pt0) REVERT: A 278 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9167 (p) REVERT: A 342 LEU cc_start: 0.9624 (mt) cc_final: 0.9268 (tp) REVERT: A 369 LEU cc_start: 0.9597 (tp) cc_final: 0.9346 (tt) REVERT: A 475 MET cc_start: 0.9007 (tpp) cc_final: 0.8366 (tpp) REVERT: A 478 ASN cc_start: 0.9371 (m-40) cc_final: 0.8982 (p0) REVERT: B 654 GLU cc_start: 0.9603 (tm-30) cc_final: 0.9280 (pp20) REVERT: B 657 GLU cc_start: 0.9619 (tt0) cc_final: 0.9337 (tm-30) REVERT: C 95 MET cc_start: 0.9211 (ptm) cc_final: 0.8355 (tmm) REVERT: C 121 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8942 (tptp) REVERT: C 190 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8758 (pm20) REVERT: C 369 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9216 (tt) REVERT: C 374 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7452 (t-90) REVERT: D 579 ARG cc_start: 0.8195 (mtm-85) cc_final: 0.7849 (mtm-85) REVERT: D 626 MET cc_start: 0.9344 (mmm) cc_final: 0.8769 (tpp) REVERT: D 630 GLN cc_start: 0.9738 (OUTLIER) cc_final: 0.9359 (mt0) REVERT: D 632 ASP cc_start: 0.9685 (t0) cc_final: 0.9404 (m-30) REVERT: D 661 LEU cc_start: 0.9609 (tt) cc_final: 0.9374 (pp) REVERT: E 104 MET cc_start: 0.9656 (OUTLIER) cc_final: 0.9432 (ptm) REVERT: E 127 VAL cc_start: 0.9708 (OUTLIER) cc_final: 0.9389 (m) REVERT: E 161 MET cc_start: 0.8665 (mmm) cc_final: 0.8360 (tmm) REVERT: E 166 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8357 (ttp80) REVERT: E 369 LEU cc_start: 0.9515 (tp) cc_final: 0.9165 (tt) REVERT: E 434 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8129 (tmm) REVERT: E 475 MET cc_start: 0.9397 (tpp) cc_final: 0.9170 (tpp) REVERT: F 542 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8690 (ttm110) REVERT: F 589 ASP cc_start: 0.9102 (m-30) cc_final: 0.8626 (p0) REVERT: F 626 MET cc_start: 0.8654 (tpp) cc_final: 0.8268 (tpp) REVERT: H 3 GLN cc_start: 0.8994 (pm20) cc_final: 0.8301 (pm20) REVERT: H 4 LEU cc_start: 0.7999 (mt) cc_final: 0.7238 (tp) REVERT: H 76 ASN cc_start: 0.9077 (p0) cc_final: 0.8646 (p0) REVERT: H 100 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9075 (t) REVERT: I 3 GLN cc_start: 0.8962 (pm20) cc_final: 0.8433 (pm20) REVERT: I 4 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7956 (tt) REVERT: I 52 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.8853 (t) REVERT: I 55 LYS cc_start: 0.9552 (OUTLIER) cc_final: 0.9273 (ttpt) REVERT: I 76 ASN cc_start: 0.9034 (m-40) cc_final: 0.8793 (p0) REVERT: J 3 GLN cc_start: 0.9152 (pm20) cc_final: 0.8533 (pm20) REVERT: J 4 LEU cc_start: 0.8844 (mt) cc_final: 0.8379 (tt) REVERT: J 37 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8668 (t80) REVERT: J 76 ASN cc_start: 0.9186 (p0) cc_final: 0.8787 (p0) outliers start: 76 outliers final: 35 residues processed: 243 average time/residue: 0.2779 time to fit residues: 102.8301 Evaluate side-chains 212 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 205 CYS 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 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 116 LEU Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 190 GLU 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 326 ILE 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 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 104 MET Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 202 THR 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 433 CYS Chi-restraints excluded: chain E residue 434 MET 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 52 SER Chi-restraints excluded: chain I residue 55 LYS Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 87 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: 6.9990 chunk 2 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.043042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.031493 restraints weight = 101296.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.032823 restraints weight = 55458.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.033756 restraints weight = 37981.629| |-----------------------------------------------------------------------------| r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 17943 Z= 0.273 Angle : 0.795 14.185 24493 Z= 0.391 Chirality : 0.046 0.280 2922 Planarity : 0.004 0.063 3009 Dihedral : 8.852 109.084 3830 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 11.09 % Favored : 88.52 % Rotamer: Outliers : 4.66 % Allowed : 28.07 % 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: -2.25 (0.18), residues: 2065 helix: -0.29 (0.29), residues: 339 sheet: -0.34 (0.24), residues: 457 loop : -2.43 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 479 HIS 0.003 0.001 HIS A 105 PHE 0.024 0.002 PHE J 27 TYR 0.015 0.001 TYR E 39 ARG 0.010 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00543 ( 49) link_NAG-ASN : angle 2.72206 ( 147) link_BETA1-4 : bond 0.00213 ( 25) link_BETA1-4 : angle 1.54120 ( 75) link_ALPHA1-3 : bond 0.00536 ( 2) link_ALPHA1-3 : angle 2.51763 ( 6) hydrogen bonds : bond 0.03939 ( 419) hydrogen bonds : angle 5.06935 ( 1101) SS BOND : bond 0.00438 ( 42) SS BOND : angle 1.53968 ( 84) covalent geometry : bond 0.00583 (17825) covalent geometry : angle 0.76059 (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 234 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 149 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9204 (ptm) cc_final: 0.8895 (ptm) REVERT: A 104 MET cc_start: 0.9377 (ptm) cc_final: 0.9003 (tmm) REVERT: A 125 LEU cc_start: 0.9720 (tp) cc_final: 0.9462 (mm) REVERT: A 258 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: A 342 LEU cc_start: 0.9667 (mt) cc_final: 0.9215 (tp) REVERT: A 475 MET cc_start: 0.9144 (tpp) cc_final: 0.8501 (tpp) REVERT: A 478 ASN cc_start: 0.9378 (m-40) cc_final: 0.8880 (p0) REVERT: B 589 ASP cc_start: 0.9121 (m-30) cc_final: 0.8879 (p0) REVERT: B 654 GLU cc_start: 0.9700 (tm-30) cc_final: 0.9335 (tm-30) REVERT: B 657 GLU cc_start: 0.9617 (tt0) cc_final: 0.9361 (tm-30) REVERT: C 95 MET cc_start: 0.9255 (ptm) cc_final: 0.8556 (tmm) REVERT: C 104 MET cc_start: 0.9670 (ptm) cc_final: 0.9296 (tmm) REVERT: C 121 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9143 (tptp) REVERT: C 161 MET cc_start: 0.9079 (mmm) cc_final: 0.8672 (tmm) REVERT: C 190 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: C 252 LYS cc_start: 0.9611 (OUTLIER) cc_final: 0.9405 (mmmt) REVERT: C 369 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9366 (tt) REVERT: C 374 HIS cc_start: 0.8511 (OUTLIER) cc_final: 0.8042 (t-90) REVERT: C 416 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8483 (pp) REVERT: C 422 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8704 (mp10) REVERT: D 579 ARG cc_start: 0.8564 (mtm-85) cc_final: 0.7893 (mtm-85) REVERT: D 626 MET cc_start: 0.9310 (mmm) cc_final: 0.8407 (tpp) REVERT: E 104 MET cc_start: 0.9694 (OUTLIER) cc_final: 0.9246 (ppp) REVERT: E 369 LEU cc_start: 0.9648 (tp) cc_final: 0.9355 (tt) REVERT: E 434 MET cc_start: 0.8477 (tmm) cc_final: 0.8259 (tmm) REVERT: E 475 MET cc_start: 0.9344 (tpp) cc_final: 0.9135 (tpt) REVERT: F 542 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8820 (ttm110) REVERT: F 603 ILE cc_start: 0.9077 (pt) cc_final: 0.8639 (pt) REVERT: F 626 MET cc_start: 0.8988 (tpp) cc_final: 0.8529 (tpp) REVERT: F 657 GLU cc_start: 0.9457 (tt0) cc_final: 0.9057 (pt0) REVERT: H 2 VAL cc_start: 0.8221 (OUTLIER) cc_final: 0.7669 (t) REVERT: H 3 GLN cc_start: 0.9070 (pm20) cc_final: 0.8481 (pm20) REVERT: H 4 LEU cc_start: 0.8116 (mt) cc_final: 0.7670 (mt) REVERT: H 76 ASN cc_start: 0.9138 (p0) cc_final: 0.8736 (p0) REVERT: H 82 MET cc_start: 0.9547 (mmm) cc_final: 0.9325 (mmm) REVERT: H 100 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.9082 (t) REVERT: I 3 GLN cc_start: 0.9055 (pm20) cc_final: 0.8777 (pm20) REVERT: I 55 LYS cc_start: 0.9595 (OUTLIER) cc_final: 0.9342 (ttpt) REVERT: I 76 ASN cc_start: 0.9130 (m-40) cc_final: 0.8899 (p0) REVERT: J 3 GLN cc_start: 0.9269 (pm20) cc_final: 0.8760 (pm20) REVERT: J 4 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8411 (tt) REVERT: J 37 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8601 (t80) REVERT: J 76 ASN cc_start: 0.9163 (p0) cc_final: 0.8713 (p0) outliers start: 85 outliers final: 51 residues processed: 225 average time/residue: 0.2837 time to fit residues: 97.4058 Evaluate side-chains 205 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 140 time to evaluate : 1.930 ------------------------------------------------------------------------------- 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 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 C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 116 LEU 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 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 252 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 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 630 GLN 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 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 660 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 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 Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 168 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 137 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.043611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.032021 restraints weight = 99582.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033369 restraints weight = 54797.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.034329 restraints weight = 37440.151| |-----------------------------------------------------------------------------| r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17943 Z= 0.155 Angle : 0.730 14.248 24493 Z= 0.359 Chirality : 0.045 0.272 2922 Planarity : 0.004 0.058 3009 Dihedral : 8.385 108.090 3829 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.46 % Favored : 89.15 % Rotamer: Outliers : 4.17 % Allowed : 27.85 % Favored : 67.98 % 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: -2.15 (0.18), residues: 2065 helix: -0.13 (0.29), residues: 343 sheet: -0.40 (0.24), residues: 482 loop : -2.36 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 623 HIS 0.003 0.001 HIS A 105 PHE 0.012 0.001 PHE J 27 TYR 0.013 0.001 TYR E 39 ARG 0.012 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 49) link_NAG-ASN : angle 2.56821 ( 147) link_BETA1-4 : bond 0.00276 ( 25) link_BETA1-4 : angle 1.19808 ( 75) link_ALPHA1-3 : bond 0.00815 ( 2) link_ALPHA1-3 : angle 2.63270 ( 6) hydrogen bonds : bond 0.03495 ( 419) hydrogen bonds : angle 4.77028 ( 1101) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.43117 ( 84) covalent geometry : bond 0.00343 (17825) covalent geometry : angle 0.69719 (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 231 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 155 time to evaluate : 2.101 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: 0.9331 (OUTLIER) cc_final: 0.8964 (t) REVERT: A 95 MET cc_start: 0.9207 (ptm) cc_final: 0.8850 (ptm) REVERT: A 104 MET cc_start: 0.9400 (ptm) cc_final: 0.8799 (ppp) REVERT: A 125 LEU cc_start: 0.9711 (tp) cc_final: 0.9447 (mm) REVERT: A 258 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8401 (pt0) REVERT: A 475 MET cc_start: 0.9164 (tpp) cc_final: 0.8607 (tpp) REVERT: A 478 ASN cc_start: 0.9391 (m-40) cc_final: 0.8884 (p0) REVERT: B 536 THR cc_start: 0.9424 (p) cc_final: 0.9188 (t) REVERT: B 589 ASP cc_start: 0.9132 (m-30) cc_final: 0.8851 (p0) REVERT: B 654 GLU cc_start: 0.9713 (tm-30) cc_final: 0.9506 (pp20) REVERT: B 657 GLU cc_start: 0.9609 (tt0) cc_final: 0.9363 (tm-30) REVERT: C 95 MET cc_start: 0.9226 (ptm) cc_final: 0.8490 (tmm) REVERT: C 104 MET cc_start: 0.9642 (ptm) cc_final: 0.9215 (tmm) REVERT: C 121 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9123 (tptp) REVERT: C 190 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: C 258 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8779 (pt0) REVERT: C 369 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9384 (tt) REVERT: C 374 HIS cc_start: 0.8412 (OUTLIER) cc_final: 0.7866 (t-90) REVERT: C 475 MET cc_start: 0.8633 (tpt) cc_final: 0.8162 (tpt) REVERT: D 579 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7961 (mtm-85) REVERT: D 626 MET cc_start: 0.9300 (mmm) cc_final: 0.8352 (tpp) REVERT: E 40 TYR cc_start: 0.8906 (t80) cc_final: 0.8657 (t80) REVERT: E 104 MET cc_start: 0.9702 (OUTLIER) cc_final: 0.9235 (ppp) REVERT: E 125 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9274 (mm) REVERT: E 150 MET cc_start: 0.8825 (mpp) cc_final: 0.8184 (mpp) REVERT: E 166 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8469 (ttp80) REVERT: E 369 LEU cc_start: 0.9604 (tp) cc_final: 0.9335 (tt) REVERT: E 387 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8787 (p) REVERT: E 434 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8107 (tmm) REVERT: E 475 MET cc_start: 0.9350 (tpp) cc_final: 0.9105 (tpt) REVERT: F 542 ARG cc_start: 0.9056 (ttm110) cc_final: 0.8805 (ttm110) REVERT: F 589 ASP cc_start: 0.9141 (m-30) cc_final: 0.8665 (p0) REVERT: F 603 ILE cc_start: 0.8950 (pt) cc_final: 0.8714 (pt) REVERT: F 626 MET cc_start: 0.9047 (tpp) cc_final: 0.8825 (tpp) REVERT: H 2 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7627 (t) REVERT: H 3 GLN cc_start: 0.9058 (pm20) cc_final: 0.8436 (pm20) REVERT: H 4 LEU cc_start: 0.8258 (mt) cc_final: 0.7809 (mt) REVERT: H 76 ASN cc_start: 0.9149 (p0) cc_final: 0.8711 (p0) REVERT: H 100 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9035 (t) REVERT: I 3 GLN cc_start: 0.9186 (pm20) cc_final: 0.8583 (pm20) REVERT: I 4 LEU cc_start: 0.9314 (mm) cc_final: 0.8769 (mt) REVERT: J 3 GLN cc_start: 0.9276 (pm20) cc_final: 0.8713 (pm20) REVERT: J 4 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8379 (tt) REVERT: J 37 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8548 (t80) REVERT: J 76 ASN cc_start: 0.9188 (p0) cc_final: 0.8688 (p0) outliers start: 76 outliers final: 46 residues processed: 220 average time/residue: 0.3102 time to fit residues: 104.7771 Evaluate side-chains 206 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 145 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR 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 247 CYS 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 424 ILE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 116 LEU 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 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 326 ILE 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 488 VAL Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 630 GLN 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 125 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 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 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 642 ILE 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 Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 140 optimal weight: 10.0000 chunk 132 optimal weight: 0.4980 chunk 122 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.043089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.031478 restraints weight = 99607.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.032811 restraints weight = 55142.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.033768 restraints weight = 37626.930| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17943 Z= 0.190 Angle : 0.743 14.344 24493 Z= 0.365 Chirality : 0.045 0.279 2922 Planarity : 0.004 0.062 3009 Dihedral : 8.163 107.258 3828 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.70 % Favored : 88.91 % Rotamer: Outliers : 4.06 % Allowed : 28.02 % Favored : 67.93 % 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: -2.08 (0.18), residues: 2065 helix: 0.14 (0.30), residues: 322 sheet: -0.37 (0.24), residues: 478 loop : -2.33 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 96 HIS 0.004 0.001 HIS C 216 PHE 0.026 0.001 PHE J 27 TYR 0.016 0.001 TYR C 61 ARG 0.013 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 49) link_NAG-ASN : angle 2.61727 ( 147) link_BETA1-4 : bond 0.00182 ( 25) link_BETA1-4 : angle 1.30941 ( 75) link_ALPHA1-3 : bond 0.00646 ( 2) link_ALPHA1-3 : angle 2.48877 ( 6) hydrogen bonds : bond 0.03650 ( 419) hydrogen bonds : angle 4.79896 ( 1101) SS BOND : bond 0.00335 ( 42) SS BOND : angle 1.43423 ( 84) covalent geometry : bond 0.00413 (17825) covalent geometry : angle 0.70987 (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 222 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 148 time to evaluate : 1.794 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: 0.9224 (ptm) cc_final: 0.8884 (ptm) REVERT: A 104 MET cc_start: 0.9429 (ptm) cc_final: 0.8841 (ppp) REVERT: A 125 LEU cc_start: 0.9713 (tp) cc_final: 0.9446 (mm) REVERT: A 258 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: A 475 MET cc_start: 0.9190 (tpp) cc_final: 0.8697 (tpp) REVERT: A 478 ASN cc_start: 0.9369 (m-40) cc_final: 0.8878 (p0) REVERT: B 536 THR cc_start: 0.9460 (p) cc_final: 0.9240 (t) REVERT: B 589 ASP cc_start: 0.9131 (m-30) cc_final: 0.8864 (p0) REVERT: B 654 GLU cc_start: 0.9720 (tm-30) cc_final: 0.9320 (tm-30) REVERT: B 657 GLU cc_start: 0.9624 (tt0) cc_final: 0.9378 (tm-30) REVERT: C 95 MET cc_start: 0.9225 (ptm) cc_final: 0.8526 (tmm) REVERT: C 104 MET cc_start: 0.9667 (ptm) cc_final: 0.9261 (tmm) REVERT: C 121 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9142 (tptp) REVERT: C 190 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8854 (pm20) REVERT: C 258 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8765 (pt0) REVERT: C 369 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9431 (tt) REVERT: C 374 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7983 (t-90) REVERT: D 579 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: D 589 ASP cc_start: 0.9138 (m-30) cc_final: 0.8769 (p0) REVERT: D 626 MET cc_start: 0.9301 (mmm) cc_final: 0.8425 (tpp) REVERT: E 104 MET cc_start: 0.9711 (OUTLIER) cc_final: 0.9248 (ppp) REVERT: E 150 MET cc_start: 0.8847 (mpp) cc_final: 0.8232 (mpp) REVERT: E 166 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8468 (ttp80) REVERT: E 369 LEU cc_start: 0.9621 (tp) cc_final: 0.9372 (tt) REVERT: E 387 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8776 (p) REVERT: E 434 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8174 (tmm) REVERT: E 475 MET cc_start: 0.9329 (tpp) cc_final: 0.9047 (tpt) REVERT: F 542 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8885 (ttm110) REVERT: F 589 ASP cc_start: 0.9154 (m-30) cc_final: 0.8676 (p0) REVERT: F 603 ILE cc_start: 0.9078 (pt) cc_final: 0.8644 (pt) REVERT: F 626 MET cc_start: 0.9123 (tpp) cc_final: 0.8826 (tpt) REVERT: H 2 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7764 (t) REVERT: H 3 GLN cc_start: 0.8997 (pm20) cc_final: 0.8365 (pm20) REVERT: H 4 LEU cc_start: 0.8280 (mt) cc_final: 0.7798 (mt) REVERT: H 76 ASN cc_start: 0.9127 (p0) cc_final: 0.8672 (p0) REVERT: H 100 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9015 (t) REVERT: I 3 GLN cc_start: 0.9205 (pm20) cc_final: 0.8621 (pm20) REVERT: I 4 LEU cc_start: 0.9303 (mm) cc_final: 0.8775 (mt) REVERT: J 3 GLN cc_start: 0.9233 (pm20) cc_final: 0.8820 (pm20) REVERT: J 4 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8356 (tt) REVERT: J 37 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8663 (t80) REVERT: J 45 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.7835 (ptt90) REVERT: J 76 ASN cc_start: 0.9227 (p0) cc_final: 0.8722 (p0) outliers start: 74 outliers final: 46 residues processed: 214 average time/residue: 0.2791 time to fit residues: 91.2705 Evaluate side-chains 207 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 147 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 491 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 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 630 GLN 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 434 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 575 GLN 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 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 Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 155 optimal weight: 0.0050 chunk 181 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 203 optimal weight: 30.0000 chunk 85 optimal weight: 0.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 590 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.032598 restraints weight = 97867.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033964 restraints weight = 52663.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034937 restraints weight = 35760.412| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 17943 Z= 0.122 Angle : 0.748 14.278 24493 Z= 0.359 Chirality : 0.046 0.256 2922 Planarity : 0.004 0.055 3009 Dihedral : 7.861 105.799 3828 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.64 % Favored : 89.98 % Rotamer: Outliers : 3.40 % Allowed : 28.84 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.28 % 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: -1.95 (0.19), residues: 2065 helix: 0.32 (0.30), residues: 322 sheet: -0.34 (0.24), residues: 500 loop : -2.28 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 338 HIS 0.003 0.001 HIS C 216 PHE 0.014 0.001 PHE J 27 TYR 0.020 0.001 TYR C 61 ARG 0.013 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 49) link_NAG-ASN : angle 2.50602 ( 147) link_BETA1-4 : bond 0.00378 ( 25) link_BETA1-4 : angle 1.08905 ( 75) link_ALPHA1-3 : bond 0.00737 ( 2) link_ALPHA1-3 : angle 2.58947 ( 6) hydrogen bonds : bond 0.03237 ( 419) hydrogen bonds : angle 4.57324 ( 1101) SS BOND : bond 0.00332 ( 42) SS BOND : angle 1.49554 ( 84) covalent geometry : bond 0.00282 (17825) covalent geometry : angle 0.71806 (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 219 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 157 time to evaluate : 2.044 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: 0.9198 (ptm) cc_final: 0.8782 (ptm) REVERT: A 104 MET cc_start: 0.9412 (ptm) cc_final: 0.8818 (ppp) REVERT: A 125 LEU cc_start: 0.9685 (tp) cc_final: 0.9410 (mm) REVERT: A 258 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8297 (pt0) REVERT: B 536 THR cc_start: 0.9364 (p) cc_final: 0.9147 (t) REVERT: B 589 ASP cc_start: 0.9115 (m-30) cc_final: 0.8812 (p0) REVERT: B 654 GLU cc_start: 0.9713 (tm-30) cc_final: 0.9494 (pp20) REVERT: B 657 GLU cc_start: 0.9617 (tt0) cc_final: 0.9382 (tm-30) REVERT: C 95 MET cc_start: 0.9286 (ptm) cc_final: 0.8505 (tmm) REVERT: C 104 MET cc_start: 0.9660 (ptm) cc_final: 0.8958 (tmm) REVERT: C 121 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.9134 (tptp) REVERT: C 190 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8837 (pm20) REVERT: C 258 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: C 369 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9414 (tt) REVERT: C 374 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7534 (t-90) REVERT: C 475 MET cc_start: 0.8521 (tpt) cc_final: 0.8206 (tpp) REVERT: C 479 TRP cc_start: 0.9402 (m-10) cc_final: 0.8358 (m-10) REVERT: D 542 ARG cc_start: 0.9137 (ttp-110) cc_final: 0.8889 (ttm110) REVERT: D 579 ARG cc_start: 0.8453 (mtm-85) cc_final: 0.8068 (mtm-85) REVERT: D 589 ASP cc_start: 0.9168 (m-30) cc_final: 0.8775 (p0) REVERT: D 626 MET cc_start: 0.9270 (mmm) cc_final: 0.8362 (tpp) REVERT: E 104 MET cc_start: 0.9715 (OUTLIER) cc_final: 0.9476 (ptm) REVERT: E 116 LEU cc_start: 0.9363 (mt) cc_final: 0.8442 (tt) REVERT: E 150 MET cc_start: 0.8786 (mpp) cc_final: 0.8215 (mpp) REVERT: E 369 LEU cc_start: 0.9571 (tp) cc_final: 0.9360 (tt) REVERT: E 387 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.8806 (p) REVERT: F 542 ARG cc_start: 0.9113 (ttm110) cc_final: 0.8855 (ttm110) REVERT: F 575 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.9288 (pp30) REVERT: F 589 ASP cc_start: 0.9142 (m-30) cc_final: 0.8637 (p0) REVERT: F 626 MET cc_start: 0.9049 (tpp) cc_final: 0.8823 (tpp) REVERT: H 2 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7647 (t) REVERT: H 3 GLN cc_start: 0.9014 (pm20) cc_final: 0.8388 (pm20) REVERT: H 4 LEU cc_start: 0.8217 (mt) cc_final: 0.7722 (mt) REVERT: H 76 ASN cc_start: 0.9196 (p0) cc_final: 0.8760 (p0) REVERT: H 100 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8949 (t) REVERT: I 3 GLN cc_start: 0.9185 (pm20) cc_final: 0.8598 (pm20) REVERT: I 4 LEU cc_start: 0.9214 (mm) cc_final: 0.8726 (mt) REVERT: J 3 GLN cc_start: 0.9252 (pm20) cc_final: 0.8677 (pm20) REVERT: J 4 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8354 (tt) REVERT: J 37 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8656 (t80) REVERT: J 45 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8047 (ptt90) REVERT: J 76 ASN cc_start: 0.9205 (p0) cc_final: 0.8646 (p0) outliers start: 62 outliers final: 40 residues processed: 211 average time/residue: 0.2840 time to fit residues: 91.3604 Evaluate side-chains 204 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 1.883 ------------------------------------------------------------------------------- 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 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 334 SER Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 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 326 ILE 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 630 GLN Chi-restraints excluded: chain D residue 635 ILE 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 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU 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 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 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 = 0.2995 r_free = 0.2995 target = 0.043520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.031908 restraints weight = 99854.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.033272 restraints weight = 55275.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034248 restraints weight = 37725.546| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17943 Z= 0.146 Angle : 0.762 14.184 24493 Z= 0.367 Chirality : 0.045 0.297 2922 Planarity : 0.004 0.056 3009 Dihedral : 7.790 104.628 3828 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.41 % Favored : 89.20 % Rotamer: Outliers : 3.18 % Allowed : 29.11 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.92 (0.19), residues: 2065 helix: 0.35 (0.31), residues: 322 sheet: -0.22 (0.24), residues: 476 loop : -2.27 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 96 HIS 0.003 0.001 HIS C 216 PHE 0.028 0.001 PHE J 27 TYR 0.017 0.001 TYR C 61 ARG 0.014 0.000 ARG E 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00362 ( 49) link_NAG-ASN : angle 2.50750 ( 147) link_BETA1-4 : bond 0.00257 ( 25) link_BETA1-4 : angle 1.18383 ( 75) link_ALPHA1-3 : bond 0.00751 ( 2) link_ALPHA1-3 : angle 2.46312 ( 6) hydrogen bonds : bond 0.03295 ( 419) hydrogen bonds : angle 4.59346 ( 1101) SS BOND : bond 0.00431 ( 42) SS BOND : angle 1.83963 ( 84) covalent geometry : bond 0.00331 (17825) covalent geometry : angle 0.72924 (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 207 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 149 time to evaluate : 1.849 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: 0.9206 (ptm) cc_final: 0.8807 (ptm) REVERT: A 104 MET cc_start: 0.9413 (ptm) cc_final: 0.8829 (ppp) REVERT: A 258 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8326 (pt0) REVERT: A 325 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8519 (t0) REVERT: A 478 ASN cc_start: 0.9330 (m-40) cc_final: 0.8901 (p0) REVERT: B 536 THR cc_start: 0.9399 (p) cc_final: 0.9180 (t) REVERT: B 589 ASP cc_start: 0.9101 (m-30) cc_final: 0.8834 (p0) REVERT: B 654 GLU cc_start: 0.9713 (tm-30) cc_final: 0.9273 (tm-30) REVERT: B 657 GLU cc_start: 0.9622 (tt0) cc_final: 0.9387 (tm-30) REVERT: C 95 MET cc_start: 0.9301 (ptm) cc_final: 0.8514 (tmm) REVERT: C 104 MET cc_start: 0.9656 (ptm) cc_final: 0.9251 (tmm) REVERT: C 121 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.9143 (tptp) REVERT: C 150 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8220 (pmm) REVERT: C 190 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8862 (pm20) REVERT: C 258 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8666 (pt0) REVERT: C 369 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9393 (tt) REVERT: C 374 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7671 (t-90) REVERT: C 475 MET cc_start: 0.8543 (tpt) cc_final: 0.8310 (tpp) REVERT: D 542 ARG cc_start: 0.9187 (ttp-110) cc_final: 0.8942 (ttm110) REVERT: D 589 ASP cc_start: 0.9133 (m-30) cc_final: 0.8758 (p0) REVERT: D 626 MET cc_start: 0.9243 (mmm) cc_final: 0.8335 (tpp) REVERT: E 104 MET cc_start: 0.9717 (OUTLIER) cc_final: 0.9287 (ppp) REVERT: E 150 MET cc_start: 0.8791 (mpp) cc_final: 0.8227 (mpp) REVERT: E 161 MET cc_start: 0.8570 (tmm) cc_final: 0.8284 (tpp) REVERT: E 387 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8786 (p) REVERT: E 475 MET cc_start: 0.9357 (tpp) cc_final: 0.8983 (tpp) REVERT: F 542 ARG cc_start: 0.9138 (ttm110) cc_final: 0.8883 (ttm110) REVERT: F 575 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9279 (pp30) REVERT: F 589 ASP cc_start: 0.9099 (m-30) cc_final: 0.8648 (p0) REVERT: F 626 MET cc_start: 0.9082 (tpp) cc_final: 0.8842 (tpp) REVERT: H 2 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7656 (t) REVERT: H 3 GLN cc_start: 0.9025 (pm20) cc_final: 0.8409 (pm20) REVERT: H 4 LEU cc_start: 0.8256 (mt) cc_final: 0.7757 (mt) REVERT: H 76 ASN cc_start: 0.9186 (p0) cc_final: 0.8742 (p0) REVERT: H 100 THR cc_start: 0.9264 (OUTLIER) cc_final: 0.9038 (t) REVERT: I 3 GLN cc_start: 0.9191 (pm20) cc_final: 0.8714 (pm20) REVERT: J 3 GLN cc_start: 0.9255 (pm20) cc_final: 0.8844 (pm20) REVERT: J 4 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8306 (tt) REVERT: J 37 PHE cc_start: 0.8960 (OUTLIER) cc_final: 0.8715 (t80) REVERT: J 45 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7917 (ptt90) REVERT: J 76 ASN cc_start: 0.9220 (p0) cc_final: 0.8666 (p0) outliers start: 58 outliers final: 38 residues processed: 199 average time/residue: 0.2783 time to fit residues: 85.1632 Evaluate side-chains 197 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 325 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain D residue 635 ILE 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 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 18 LEU 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 45 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 156 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 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 = 0.3020 r_free = 0.3020 target = 0.044072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.032609 restraints weight = 97739.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.033972 restraints weight = 53109.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.034948 restraints weight = 35943.009| |-----------------------------------------------------------------------------| r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17943 Z= 0.129 Angle : 0.775 16.222 24493 Z= 0.368 Chirality : 0.046 0.307 2922 Planarity : 0.004 0.054 3009 Dihedral : 7.633 103.439 3828 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.17 % Favored : 89.44 % Rotamer: Outliers : 2.96 % Allowed : 29.22 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.83 (0.19), residues: 2065 helix: 0.45 (0.31), residues: 321 sheet: -0.15 (0.24), residues: 481 loop : -2.24 (0.17), residues: 1263 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 0.013 0.001 PHE E 382 TYR 0.014 0.001 TYR C 61 ARG 0.015 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00377 ( 49) link_NAG-ASN : angle 2.45957 ( 147) link_BETA1-4 : bond 0.00317 ( 25) link_BETA1-4 : angle 1.12092 ( 75) link_ALPHA1-3 : bond 0.00648 ( 2) link_ALPHA1-3 : angle 2.50122 ( 6) hydrogen bonds : bond 0.03155 ( 419) hydrogen bonds : angle 4.51137 ( 1101) SS BOND : bond 0.00310 ( 42) SS BOND : angle 1.62749 ( 84) covalent geometry : bond 0.00295 (17825) covalent geometry : angle 0.74586 (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 203 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 149 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9213 (ptm) cc_final: 0.8808 (ptm) REVERT: A 104 MET cc_start: 0.9415 (ptm) cc_final: 0.8827 (ppp) REVERT: A 258 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: B 536 THR cc_start: 0.9371 (p) cc_final: 0.9151 (t) REVERT: B 589 ASP cc_start: 0.9112 (m-30) cc_final: 0.8817 (p0) REVERT: B 654 GLU cc_start: 0.9720 (tm-30) cc_final: 0.9288 (tm-30) REVERT: C 95 MET cc_start: 0.9324 (ptm) cc_final: 0.8171 (ppp) REVERT: C 104 MET cc_start: 0.9656 (ptm) cc_final: 0.9020 (tmm) REVERT: C 121 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9141 (tptp) REVERT: C 150 MET cc_start: 0.8504 (mtm) cc_final: 0.8164 (pmm) REVERT: C 190 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8865 (pm20) REVERT: C 258 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: C 369 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9427 (tt) REVERT: C 374 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7653 (t-90) REVERT: C 475 MET cc_start: 0.8571 (tpt) cc_final: 0.8307 (tpp) REVERT: C 479 TRP cc_start: 0.9393 (m-10) cc_final: 0.8338 (m-10) REVERT: D 542 ARG cc_start: 0.9190 (ttp-110) cc_final: 0.8935 (ttm110) REVERT: D 589 ASP cc_start: 0.9161 (m-30) cc_final: 0.8783 (p0) REVERT: D 626 MET cc_start: 0.9251 (mmm) cc_final: 0.8436 (tpp) REVERT: E 104 MET cc_start: 0.9712 (OUTLIER) cc_final: 0.9294 (ppp) REVERT: E 150 MET cc_start: 0.8783 (mpp) cc_final: 0.8212 (mpp) REVERT: E 161 MET cc_start: 0.8593 (tmm) cc_final: 0.8239 (tpp) REVERT: E 271 MET cc_start: 0.7833 (mmm) cc_final: 0.7284 (mmt) REVERT: E 387 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.8824 (p) REVERT: E 475 MET cc_start: 0.9347 (tpp) cc_final: 0.8945 (tpp) REVERT: F 542 ARG cc_start: 0.9113 (ttm110) cc_final: 0.8864 (ttm110) REVERT: F 575 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9272 (pp30) REVERT: F 589 ASP cc_start: 0.9092 (m-30) cc_final: 0.8618 (p0) REVERT: F 626 MET cc_start: 0.9028 (tpp) cc_final: 0.8496 (tpp) REVERT: H 2 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7610 (t) REVERT: H 3 GLN cc_start: 0.9007 (pm20) cc_final: 0.8363 (pm20) REVERT: H 4 LEU cc_start: 0.8206 (mt) cc_final: 0.7704 (mt) REVERT: H 76 ASN cc_start: 0.9197 (p0) cc_final: 0.8773 (p0) REVERT: I 3 GLN cc_start: 0.9083 (pm20) cc_final: 0.8596 (pm20) REVERT: I 76 ASN cc_start: 0.9205 (m-40) cc_final: 0.8937 (p0) REVERT: J 3 GLN cc_start: 0.9239 (pm20) cc_final: 0.8822 (pm20) REVERT: J 4 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8292 (tt) REVERT: J 37 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8535 (t80) REVERT: J 76 ASN cc_start: 0.9225 (p0) cc_final: 0.8659 (p0) outliers start: 54 outliers final: 36 residues processed: 195 average time/residue: 0.2725 time to fit residues: 82.9573 Evaluate side-chains 194 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 2.103 ------------------------------------------------------------------------------- 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 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 334 SER Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 121 LYS Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 202 THR 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 258 GLN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 369 LEU 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 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 320 THR Chi-restraints excluded: chain E residue 385 CYS Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain F residue 571 TRP Chi-restraints excluded: chain F residue 575 GLN 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 100 VAL Chi-restraints excluded: chain J residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 70 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 46 optimal weight: 0.0970 chunk 184 optimal weight: 0.0010 chunk 191 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 121 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 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 = 0.3047 r_free = 0.3047 target = 0.044757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.033330 restraints weight = 97228.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.034721 restraints weight = 51831.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.035686 restraints weight = 34844.176| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17943 Z= 0.120 Angle : 0.766 14.147 24493 Z= 0.365 Chirality : 0.046 0.268 2922 Planarity : 0.004 0.055 3009 Dihedral : 7.449 101.381 3828 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.49 % Favored : 90.12 % Rotamer: Outliers : 2.96 % Allowed : 29.11 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -1.75 (0.19), residues: 2065 helix: 0.35 (0.30), residues: 333 sheet: -0.08 (0.24), residues: 487 loop : -2.16 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 35 HIS 0.003 0.001 HIS C 216 PHE 0.026 0.001 PHE J 27 TYR 0.014 0.001 TYR C 61 ARG 0.015 0.000 ARG B 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 49) link_NAG-ASN : angle 2.41256 ( 147) link_BETA1-4 : bond 0.00343 ( 25) link_BETA1-4 : angle 1.08374 ( 75) link_ALPHA1-3 : bond 0.00710 ( 2) link_ALPHA1-3 : angle 2.47080 ( 6) hydrogen bonds : bond 0.03082 ( 419) hydrogen bonds : angle 4.46458 ( 1101) SS BOND : bond 0.00319 ( 42) SS BOND : angle 1.67004 ( 84) covalent geometry : bond 0.00277 (17825) covalent geometry : angle 0.73815 (24181) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5092.65 seconds wall clock time: 90 minutes 27.18 seconds (5427.18 seconds total)