Starting phenix.real_space_refine on Wed Jun 18 22:13:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.map" model { file = "/net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mep_23801/06_2025/7mep_23801.cif" } resolution = 3.5 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= 0.000 sd= 0.002 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 128 5.16 5 C 13518 2.51 5 N 3635 2.21 5 O 4355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21636 Number of models: 1 Model: "" Number of chains: 35 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "I" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3477 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "H" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 995 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain: "M" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 817 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "N" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "D" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 985 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 13.34, per 1000 atoms: 0.62 Number of scatterers: 21636 At special positions: 0 Unit cell: (130.81, 126.69, 172.01, 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 128 16.00 O 4355 8.00 N 3635 7.00 C 13518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.02 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.06 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " 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 O 3 " - " MAN O 4 " " BMA U 3 " - " MAN U 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA O 3 " - " MAN O 5 " " BMA U 3 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 386 " " NAG C 705 " - " ASN C 363 " " NAG C 706 " - " ASN C 234 " " NAG C 707 " - " ASN C 197 " " NAG C 708 " - " ASN C 133 " " NAG C 709 " - " ASN C 301 " " NAG C 710 " - " ASN C 88 " " NAG C 711 " - " ASN C 241 " " NAG C 712 " - " ASN C 289 " " NAG C 713 " - " ASN C 339 " " NAG C 714 " - " ASN C 355 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 160 " " NAG D 702 " - " ASN D 276 " " NAG D 703 " - " ASN D 295 " " NAG D 704 " - " ASN D 386 " " NAG D 705 " - " ASN D 363 " " NAG D 706 " - " ASN D 234 " " NAG D 707 " - " ASN D 197 " " NAG D 708 " - " ASN D 133 " " NAG D 709 " - " ASN D 88 " " NAG D 710 " - " ASN D 241 " " NAG D 711 " - " ASN D 289 " " NAG D 712 " - " ASN D 339 " " NAG D 713 " - " ASN D 355 " " NAG D 714 " - " ASN D 392 " " NAG E 701 " - " ASN E 637 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 611 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 448 " " NAG Q 1 " - " ASN A 295 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 301 " " NAG T 1 " - " ASN A 332 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 295 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN D 262 " " NAG Z 1 " - " ASN D 448 " " NAG a 1 " - " ASN D 156 " " NAG b 1 " - " ASN D 301 " " NAG c 1 " - " ASN D 332 " Time building additional restraints: 5.46 Conformation dependent library (CDL) restraints added in 2.7 seconds 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 49 sheets defined 21.3% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.448A pdb=" N SER I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.099A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.833A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.600A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.416A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 541 removed outlier: 5.869A pdb=" N THR B 538 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 539 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.838A 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 657 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.931A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.084A pdb=" N VAL L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.403A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.156A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.889A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.976A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.407A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.524A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.769A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 657 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.728A pdb=" N VAL K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 65 removed outlier: 5.320A pdb=" N SER N 65 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.518A pdb=" N THR N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.122A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.005A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 475 through 484 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 535 through 541 removed outlier: 5.813A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL F 539 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.747A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 658 Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.491A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA G 84 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AA4, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 57 through 59 removed outlier: 3.828A pdb=" N GLY I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR I 40 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.396A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.515A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.413A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.125A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.839A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.751A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.841A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.590A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.623A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 57 through 59 removed outlier: 4.845A pdb=" N GLY M 44 " --> pdb=" O THR M 40 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR M 50 " --> pdb=" O TRP M 35 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O TYR M 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.916A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AD1, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.332A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AD4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.569A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.276A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.956A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.978A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.364A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.718A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.123A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.523A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.903A pdb=" N ALA K 84 " --> pdb=" O VAL K 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 57 through 59 removed outlier: 4.068A pdb=" N GLY N 44 " --> pdb=" O THR N 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR N 40 " --> pdb=" O GLY N 44 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR N 50 " --> pdb=" O TRP N 35 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TRP N 35 " --> pdb=" O TYR N 50 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 494 through 499 removed outlier: 5.345A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE7, first strand: chain 'D' and resid 75 through 76 removed outlier: 4.074A pdb=" N VAL D 75 " --> pdb=" O CYS D 54 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE9, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AF1, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.523A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 394 through 395 removed outlier: 6.259A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.997A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER D 334 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR D 450 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ASN D 448 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.667A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 10.131A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.018A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.659A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) 917 hydrogen bonds defined for protein. 2370 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: 8.50 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5042 1.32 - 1.46: 6975 1.46 - 1.59: 9820 1.59 - 1.73: 86 1.73 - 1.87: 157 Bond restraints: 22080 Sorted by residual: bond pdb=" NE ARG C 504 " pdb=" CZ ARG C 504 " ideal model delta sigma weight residual 1.326 1.414 -0.088 1.10e-02 8.26e+03 6.37e+01 bond pdb=" NE ARG K 3 " pdb=" CZ ARG K 3 " ideal model delta sigma weight residual 1.326 1.405 -0.079 1.10e-02 8.26e+03 5.11e+01 bond pdb=" CG GLN K 6 " pdb=" CD GLN K 6 " ideal model delta sigma weight residual 1.516 1.353 0.163 2.50e-02 1.60e+03 4.23e+01 bond pdb=" NE ARG J 3 " pdb=" CZ ARG J 3 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.07e+01 bond pdb=" NE1 TRP I 96 " pdb=" CE2 TRP I 96 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.71e+01 ... (remaining 22075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 26499 2.64 - 5.28: 3102 5.28 - 7.92: 370 7.92 - 10.56: 30 10.56 - 13.20: 1 Bond angle restraints: 30002 Sorted by residual: angle pdb=" N ASP B 659 " pdb=" CA ASP B 659 " pdb=" C ASP B 659 " ideal model delta sigma weight residual 111.28 120.99 -9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 128.55 -8.99 1.02e+00 9.61e-01 7.76e+01 angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.53 -8.97 1.02e+00 9.61e-01 7.74e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.01e+00 9.80e-01 6.88e+01 angle pdb=" C GLU D 492 " pdb=" N PRO D 493 " pdb=" CA PRO D 493 " ideal model delta sigma weight residual 119.56 127.96 -8.40 1.02e+00 9.61e-01 6.78e+01 ... (remaining 29997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.19: 13875 21.19 - 42.39: 295 42.39 - 63.58: 103 63.58 - 84.77: 47 84.77 - 105.96: 17 Dihedral angle restraints: 14337 sinusoidal: 6874 harmonic: 7463 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.59 -66.59 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.48 -66.48 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 154.78 -61.78 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 14334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2470 0.111 - 0.222: 758 0.222 - 0.333: 236 0.333 - 0.444: 127 0.444 - 0.555: 24 Chirality restraints: 3615 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 3612 not shown) Planarity restraints: 3772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 706 " -0.226 2.00e-02 2.50e+03 1.89e-01 4.45e+02 pdb=" C7 NAG D 706 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG D 706 " -0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 706 " 0.312 2.00e-02 2.50e+03 pdb=" O7 NAG D 706 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " -0.172 2.00e-02 2.50e+03 1.42e-01 2.53e+02 pdb=" C7 NAG S 2 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.126 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " 0.230 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 706 " 0.164 2.00e-02 2.50e+03 1.39e-01 2.40e+02 pdb=" C7 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C 706 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG C 706 " -0.224 2.00e-02 2.50e+03 pdb=" O7 NAG C 706 " 0.130 2.00e-02 2.50e+03 ... (remaining 3769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5522 2.81 - 3.34: 19305 3.34 - 3.86: 35748 3.86 - 4.38: 42425 4.38 - 4.90: 69566 Nonbonded interactions: 172566 Sorted by model distance: nonbonded pdb=" O3 NAG E 702 " pdb=" O7 NAG E 702 " model vdw 2.293 3.040 nonbonded pdb=" N GLY L 50 " pdb=" O GLY L 50 " model vdw 2.370 2.496 nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.385 3.040 nonbonded pdb=" NZ LYS A 207 " pdb=" OD2 ASP H 100C" model vdw 2.411 3.120 nonbonded pdb=" N ILE D 213 " pdb=" O ILE D 213 " model vdw 2.420 2.496 ... (remaining 172561 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 33 through 504 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 702 through 714)) selection = (chain 'D' and (resid 33 through 57 or resid 66 through 185 or resid 189 through \ 504 or resid 701 through 713)) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 3 through 106) selection = chain 'J' selection = (chain 'K' and resid 3 through 106) } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 50.130 Find NCS groups from input model: 1.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.024 0.163 22211 Z= 1.256 Angle : 1.765 13.201 30354 Z= 1.143 Chirality : 0.138 0.555 3615 Planarity : 0.010 0.189 3706 Dihedral : 11.264 105.964 9408 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.77 (0.16), residues: 2544 helix: -0.29 (0.22), residues: 447 sheet: 0.92 (0.17), residues: 749 loop : 0.73 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.009 TRP J 94 HIS 0.012 0.002 HIS A 374 PHE 0.032 0.006 PHE G 71 TYR 0.057 0.007 TYR I 99 ARG 0.008 0.001 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.07825 ( 66) link_NAG-ASN : angle 2.80073 ( 198) link_ALPHA1-6 : bond 0.05523 ( 3) link_ALPHA1-6 : angle 2.53294 ( 9) link_BETA1-4 : bond 0.07131 ( 18) link_BETA1-4 : angle 4.74893 ( 54) link_ALPHA1-3 : bond 0.08780 ( 3) link_ALPHA1-3 : angle 4.95621 ( 9) hydrogen bonds : bond 0.16129 ( 839) hydrogen bonds : angle 7.83157 ( 2370) SS BOND : bond 0.01044 ( 41) SS BOND : angle 2.64611 ( 82) covalent geometry : bond 0.02357 (22080) covalent geometry : angle 1.74087 (30002) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 82 ASP cc_start: 0.6977 (m-30) cc_final: 0.6200 (p0) REVERT: I 18 LEU cc_start: 0.8262 (mt) cc_final: 0.8019 (tp) REVERT: A 74 CYS cc_start: 0.8044 (p) cc_final: 0.7517 (t) REVERT: A 125 LEU cc_start: 0.9178 (mt) cc_final: 0.8972 (mt) REVERT: A 161 MET cc_start: 0.8663 (tpt) cc_final: 0.8094 (tpt) REVERT: A 198 THR cc_start: 0.9220 (m) cc_final: 0.9016 (p) REVERT: A 430 ILE cc_start: 0.9041 (mm) cc_final: 0.8778 (tp) REVERT: H 102 SER cc_start: 0.9118 (m) cc_final: 0.8840 (m) REVERT: M 32 ASN cc_start: 0.8006 (m-40) cc_final: 0.7349 (m-40) REVERT: M 101 ASP cc_start: 0.7810 (m-30) cc_final: 0.7584 (p0) REVERT: C 161 MET cc_start: 0.8726 (tpt) cc_final: 0.8505 (tpt) REVERT: K 69 THR cc_start: 0.6183 (p) cc_final: 0.5846 (t) REVERT: K 85 VAL cc_start: 0.8298 (t) cc_final: 0.8059 (p) REVERT: K 92 ASN cc_start: 0.8609 (p0) cc_final: 0.7366 (t0) REVERT: N 101 ASP cc_start: 0.8474 (m-30) cc_final: 0.7947 (m-30) REVERT: D 109 ILE cc_start: 0.9489 (mm) cc_final: 0.9270 (mt) REVERT: D 257 THR cc_start: 0.9299 (p) cc_final: 0.8960 (t) REVERT: F 659 ASP cc_start: 0.8672 (t70) cc_final: 0.8425 (t0) outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.3948 time to fit residues: 335.0515 Evaluate side-chains 308 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 213 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS B 577 GLN H 105 GLN L 3 GLN L 32 GLN L 79 GLN J 42 GLN C 280 ASN C 300 ASN C 352 HIS K 38 GLN ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN D 66 HIS D 300 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098367 restraints weight = 37226.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101118 restraints weight = 20967.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102849 restraints weight = 14515.637| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22211 Z= 0.182 Angle : 0.761 11.514 30354 Z= 0.383 Chirality : 0.051 0.338 3615 Planarity : 0.005 0.043 3706 Dihedral : 7.934 74.257 4652 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.35 % Allowed : 8.04 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.03 (0.16), residues: 2544 helix: 1.54 (0.27), residues: 409 sheet: 0.90 (0.18), residues: 749 loop : 0.42 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 96 HIS 0.004 0.001 HIS E 570 PHE 0.021 0.002 PHE G 98 TYR 0.017 0.002 TYR N 91 ARG 0.007 0.001 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00401 ( 66) link_NAG-ASN : angle 2.92780 ( 198) link_ALPHA1-6 : bond 0.00598 ( 3) link_ALPHA1-6 : angle 1.45137 ( 9) link_BETA1-4 : bond 0.00732 ( 18) link_BETA1-4 : angle 2.73783 ( 54) link_ALPHA1-3 : bond 0.01022 ( 3) link_ALPHA1-3 : angle 2.70001 ( 9) hydrogen bonds : bond 0.05483 ( 839) hydrogen bonds : angle 5.90008 ( 2370) SS BOND : bond 0.00386 ( 41) SS BOND : angle 1.08356 ( 82) covalent geometry : bond 0.00415 (22080) covalent geometry : angle 0.71449 (30002) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 389 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 96 TRP cc_start: 0.7856 (m-10) cc_final: 0.7533 (m-10) REVERT: I 18 LEU cc_start: 0.8195 (mt) cc_final: 0.7946 (tp) REVERT: A 74 CYS cc_start: 0.7223 (p) cc_final: 0.6879 (t) REVERT: A 430 ILE cc_start: 0.8979 (mm) cc_final: 0.8581 (tp) REVERT: B 535 MET cc_start: 0.7916 (mmp) cc_final: 0.7575 (mmt) REVERT: J 105 GLU cc_start: 0.6122 (tp30) cc_final: 0.5826 (tp30) REVERT: M 27 ASP cc_start: 0.5489 (t70) cc_final: 0.4660 (t70) REVERT: M 32 ASN cc_start: 0.7759 (m-40) cc_final: 0.6864 (m-40) REVERT: E 542 ARG cc_start: 0.7839 (mtm-85) cc_final: 0.7539 (mmm160) REVERT: E 661 LEU cc_start: 0.8002 (tp) cc_final: 0.7481 (mt) REVERT: K 85 VAL cc_start: 0.8075 (t) cc_final: 0.7748 (p) REVERT: K 92 ASN cc_start: 0.8034 (p0) cc_final: 0.7569 (t0) REVERT: N 33 ASN cc_start: 0.8178 (t0) cc_final: 0.7887 (t0) REVERT: N 43 LYS cc_start: 0.7627 (mtmt) cc_final: 0.6256 (mtpp) REVERT: N 81 LYS cc_start: 0.6823 (mptt) cc_final: 0.6553 (tttp) REVERT: N 101 ASP cc_start: 0.8162 (m-30) cc_final: 0.7700 (m-30) REVERT: D 257 THR cc_start: 0.9155 (p) cc_final: 0.8860 (t) outliers start: 31 outliers final: 19 residues processed: 406 average time/residue: 0.3674 time to fit residues: 224.6489 Evaluate side-chains 322 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 303 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 107 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 244 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 103 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 223 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN E 658 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.118407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096469 restraints weight = 37135.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099118 restraints weight = 21317.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100784 restraints weight = 14953.731| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22211 Z= 0.166 Angle : 0.656 8.646 30354 Z= 0.331 Chirality : 0.048 0.328 3615 Planarity : 0.004 0.044 3706 Dihedral : 7.033 63.192 4652 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.10 % Allowed : 8.65 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.86 (0.16), residues: 2544 helix: 1.66 (0.27), residues: 415 sheet: 0.85 (0.18), residues: 791 loop : 0.13 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 47 HIS 0.004 0.001 HIS E 585 PHE 0.016 0.002 PHE I 78 TYR 0.020 0.002 TYR J 49 ARG 0.007 0.001 ARG M 13 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 66) link_NAG-ASN : angle 2.41962 ( 198) link_ALPHA1-6 : bond 0.00693 ( 3) link_ALPHA1-6 : angle 1.97363 ( 9) link_BETA1-4 : bond 0.00647 ( 18) link_BETA1-4 : angle 1.91672 ( 54) link_ALPHA1-3 : bond 0.01124 ( 3) link_ALPHA1-3 : angle 1.79428 ( 9) hydrogen bonds : bond 0.04671 ( 839) hydrogen bonds : angle 5.37849 ( 2370) SS BOND : bond 0.00365 ( 41) SS BOND : angle 0.98445 ( 82) covalent geometry : bond 0.00390 (22080) covalent geometry : angle 0.62041 (30002) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 348 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8994 (pttt) cc_final: 0.8418 (pttt) REVERT: A 74 CYS cc_start: 0.7224 (p) cc_final: 0.6862 (t) REVERT: A 110 SER cc_start: 0.9057 (t) cc_final: 0.8608 (m) REVERT: A 161 MET cc_start: 0.8195 (tpp) cc_final: 0.7978 (tpt) REVERT: A 430 ILE cc_start: 0.9065 (mm) cc_final: 0.8633 (tp) REVERT: B 621 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 625 ASN cc_start: 0.8083 (m-40) cc_final: 0.7878 (p0) REVERT: M 13 ARG cc_start: 0.5719 (mmm160) cc_final: 0.5050 (mmp-170) REVERT: M 27 ASP cc_start: 0.5791 (t70) cc_final: 0.4674 (t0) REVERT: M 32 ASN cc_start: 0.7796 (m-40) cc_final: 0.6887 (m110) REVERT: M 48 ILE cc_start: 0.7078 (mp) cc_final: 0.6812 (tp) REVERT: M 89 LYS cc_start: 0.7787 (tptp) cc_final: 0.7382 (tptp) REVERT: E 588 ARG cc_start: 0.7999 (ttt90) cc_final: 0.7734 (ttt-90) REVERT: E 634 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7388 (tm-30) REVERT: K 85 VAL cc_start: 0.8182 (t) cc_final: 0.7882 (p) REVERT: K 92 ASN cc_start: 0.8241 (p0) cc_final: 0.7475 (t0) REVERT: N 5 VAL cc_start: 0.7099 (p) cc_final: 0.6817 (t) REVERT: N 32 ASN cc_start: 0.8999 (m-40) cc_final: 0.8317 (m110) REVERT: N 33 ASN cc_start: 0.8317 (t0) cc_final: 0.8020 (t0) REVERT: N 43 LYS cc_start: 0.7580 (mtmt) cc_final: 0.6215 (mtpp) REVERT: N 101 ASP cc_start: 0.8154 (m-30) cc_final: 0.7763 (m-30) REVERT: D 46 LYS cc_start: 0.8613 (pttt) cc_final: 0.8382 (pttm) outliers start: 48 outliers final: 32 residues processed: 373 average time/residue: 0.3714 time to fit residues: 208.5263 Evaluate side-chains 326 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 294 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 161 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 84 optimal weight: 0.1980 chunk 194 optimal weight: 10.0000 chunk 193 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN L 3 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095060 restraints weight = 37618.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097700 restraints weight = 21516.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.099378 restraints weight = 15015.423| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22211 Z= 0.171 Angle : 0.634 8.442 30354 Z= 0.317 Chirality : 0.047 0.337 3615 Planarity : 0.004 0.045 3706 Dihedral : 6.625 56.281 4652 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.32 % Allowed : 9.88 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.70 (0.16), residues: 2544 helix: 1.66 (0.27), residues: 415 sheet: 0.76 (0.18), residues: 797 loop : -0.03 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.004 0.001 HIS D 105 PHE 0.015 0.002 PHE K 98 TYR 0.018 0.002 TYR J 49 ARG 0.006 0.001 ARG N 100B Details of bonding type rmsd link_NAG-ASN : bond 0.00314 ( 66) link_NAG-ASN : angle 2.30718 ( 198) link_ALPHA1-6 : bond 0.00372 ( 3) link_ALPHA1-6 : angle 1.94362 ( 9) link_BETA1-4 : bond 0.00488 ( 18) link_BETA1-4 : angle 1.81494 ( 54) link_ALPHA1-3 : bond 0.01035 ( 3) link_ALPHA1-3 : angle 2.45611 ( 9) hydrogen bonds : bond 0.04412 ( 839) hydrogen bonds : angle 5.23200 ( 2370) SS BOND : bond 0.00355 ( 41) SS BOND : angle 1.00765 ( 82) covalent geometry : bond 0.00405 (22080) covalent geometry : angle 0.59942 (30002) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 319 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.7262 (p) cc_final: 0.6882 (t) REVERT: A 110 SER cc_start: 0.9134 (t) cc_final: 0.8699 (m) REVERT: A 430 ILE cc_start: 0.9011 (mm) cc_final: 0.8680 (tp) REVERT: B 625 ASN cc_start: 0.8105 (m-40) cc_final: 0.7844 (p0) REVERT: M 27 ASP cc_start: 0.6082 (t70) cc_final: 0.4886 (t0) REVERT: M 32 ASN cc_start: 0.7936 (m-40) cc_final: 0.7304 (m110) REVERT: M 89 LYS cc_start: 0.7843 (tptp) cc_final: 0.7400 (tptp) REVERT: C 128 THR cc_start: 0.9090 (m) cc_final: 0.8883 (p) REVERT: E 588 ARG cc_start: 0.8083 (ttt90) cc_final: 0.7818 (ttt-90) REVERT: E 634 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7462 (tm-30) REVERT: E 655 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8388 (mttp) REVERT: K 92 ASN cc_start: 0.8318 (p0) cc_final: 0.7553 (t0) REVERT: N 5 VAL cc_start: 0.7205 (p) cc_final: 0.6936 (t) REVERT: N 33 ASN cc_start: 0.8387 (t0) cc_final: 0.8137 (t0) REVERT: N 43 LYS cc_start: 0.7609 (mtmt) cc_final: 0.6209 (mtpp) outliers start: 53 outliers final: 41 residues processed: 352 average time/residue: 0.3711 time to fit residues: 197.5561 Evaluate side-chains 335 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 293 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 71 THR Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 232 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 252 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 218 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 32 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN K 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.095703 restraints weight = 37416.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098368 restraints weight = 21313.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100066 restraints weight = 14892.472| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22211 Z= 0.119 Angle : 0.581 7.612 30354 Z= 0.290 Chirality : 0.046 0.306 3615 Planarity : 0.004 0.045 3706 Dihedral : 6.116 58.819 4652 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.84 % Allowed : 11.10 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.17), residues: 2544 helix: 1.67 (0.27), residues: 427 sheet: 0.72 (0.17), residues: 812 loop : -0.08 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 36 HIS 0.003 0.001 HIS C 374 PHE 0.012 0.002 PHE N 100C TYR 0.013 0.001 TYR J 49 ARG 0.003 0.000 ARG A 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 66) link_NAG-ASN : angle 2.12723 ( 198) link_ALPHA1-6 : bond 0.00361 ( 3) link_ALPHA1-6 : angle 1.73883 ( 9) link_BETA1-4 : bond 0.00491 ( 18) link_BETA1-4 : angle 1.57537 ( 54) link_ALPHA1-3 : bond 0.01173 ( 3) link_ALPHA1-3 : angle 2.05056 ( 9) hydrogen bonds : bond 0.03890 ( 839) hydrogen bonds : angle 4.99695 ( 2370) SS BOND : bond 0.00308 ( 41) SS BOND : angle 0.97617 ( 82) covalent geometry : bond 0.00273 (22080) covalent geometry : angle 0.55006 (30002) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 329 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 SER cc_start: 0.8367 (t) cc_final: 0.8041 (m) REVERT: A 74 CYS cc_start: 0.7258 (p) cc_final: 0.6825 (t) REVERT: A 110 SER cc_start: 0.9003 (t) cc_final: 0.8578 (m) REVERT: A 166 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7455 (ttp-170) REVERT: A 430 ILE cc_start: 0.8983 (mm) cc_final: 0.8677 (tp) REVERT: B 621 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7483 (mt-10) REVERT: L 31 MET cc_start: 0.8133 (mmm) cc_final: 0.7874 (mmm) REVERT: M 27 ASP cc_start: 0.6006 (t70) cc_final: 0.4702 (t0) REVERT: M 32 ASN cc_start: 0.7892 (m-40) cc_final: 0.7372 (m110) REVERT: M 89 LYS cc_start: 0.7815 (tptp) cc_final: 0.7425 (tptp) REVERT: M 108 ARG cc_start: 0.4244 (ptt180) cc_final: 0.3488 (tpp80) REVERT: E 588 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7790 (ttt-90) REVERT: E 634 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7291 (tm-30) REVERT: K 92 ASN cc_start: 0.8228 (p0) cc_final: 0.7492 (t0) REVERT: N 5 VAL cc_start: 0.7170 (p) cc_final: 0.6957 (t) REVERT: N 43 LYS cc_start: 0.7580 (mtmt) cc_final: 0.6149 (mtpp) outliers start: 42 outliers final: 30 residues processed: 353 average time/residue: 0.4018 time to fit residues: 213.1596 Evaluate side-chains 332 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 302 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain K residue 10 ILE Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 27 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 chunk 197 optimal weight: 6.9990 chunk 192 optimal weight: 0.6980 chunk 177 optimal weight: 20.0000 chunk 252 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN L 3 GLN C 85 HIS C 103 GLN K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.093882 restraints weight = 37407.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096482 restraints weight = 21526.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098132 restraints weight = 15106.034| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22211 Z= 0.184 Angle : 0.628 9.208 30354 Z= 0.312 Chirality : 0.047 0.332 3615 Planarity : 0.004 0.051 3706 Dihedral : 6.210 56.421 4652 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.49 % Allowed : 11.19 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.52 (0.16), residues: 2544 helix: 1.69 (0.27), residues: 421 sheet: 0.64 (0.18), residues: 804 loop : -0.23 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 96 HIS 0.004 0.001 HIS D 105 PHE 0.014 0.002 PHE M 78 TYR 0.019 0.002 TYR J 49 ARG 0.003 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 66) link_NAG-ASN : angle 2.16927 ( 198) link_ALPHA1-6 : bond 0.00246 ( 3) link_ALPHA1-6 : angle 1.78695 ( 9) link_BETA1-4 : bond 0.00486 ( 18) link_BETA1-4 : angle 1.71832 ( 54) link_ALPHA1-3 : bond 0.01056 ( 3) link_ALPHA1-3 : angle 2.33868 ( 9) hydrogen bonds : bond 0.04268 ( 839) hydrogen bonds : angle 5.06361 ( 2370) SS BOND : bond 0.00399 ( 41) SS BOND : angle 1.01714 ( 82) covalent geometry : bond 0.00441 (22080) covalent geometry : angle 0.59749 (30002) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 70 SER cc_start: 0.8341 (t) cc_final: 0.8002 (m) REVERT: A 74 CYS cc_start: 0.7225 (p) cc_final: 0.6933 (t) REVERT: A 110 SER cc_start: 0.9001 (t) cc_final: 0.8645 (m) REVERT: A 430 ILE cc_start: 0.9022 (mm) cc_final: 0.8750 (tp) REVERT: L 17 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6217 (m-30) REVERT: L 31 MET cc_start: 0.8141 (mmm) cc_final: 0.7922 (mmm) REVERT: M 27 ASP cc_start: 0.6038 (t70) cc_final: 0.5273 (t0) REVERT: M 32 ASN cc_start: 0.7926 (m-40) cc_final: 0.7345 (m-40) REVERT: M 89 LYS cc_start: 0.7885 (tptp) cc_final: 0.7426 (tptp) REVERT: M 108 ARG cc_start: 0.4398 (ptt180) cc_final: 0.4103 (ptt180) REVERT: E 588 ARG cc_start: 0.8129 (ttt90) cc_final: 0.7831 (ttt-90) REVERT: E 634 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7503 (tm-30) REVERT: K 92 ASN cc_start: 0.8265 (p0) cc_final: 0.7515 (t0) REVERT: N 5 VAL cc_start: 0.7239 (p) cc_final: 0.6997 (t) REVERT: N 43 LYS cc_start: 0.7503 (mtmt) cc_final: 0.6134 (mtpp) outliers start: 57 outliers final: 45 residues processed: 332 average time/residue: 0.3744 time to fit residues: 185.6025 Evaluate side-chains 337 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 291 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 88 CYS Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 51 ILE Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 158 optimal weight: 0.0980 chunk 22 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 148 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN A 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN L 3 GLN K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.118050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096549 restraints weight = 37170.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.099199 restraints weight = 21253.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100866 restraints weight = 14791.811| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22211 Z= 0.117 Angle : 0.575 10.574 30354 Z= 0.287 Chirality : 0.045 0.297 3615 Planarity : 0.004 0.046 3706 Dihedral : 5.811 55.879 4652 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.75 % Allowed : 12.11 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.59 (0.17), residues: 2544 helix: 1.82 (0.27), residues: 421 sheet: 0.67 (0.18), residues: 819 loop : -0.22 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 94 HIS 0.003 0.001 HIS C 374 PHE 0.013 0.001 PHE I 100C TYR 0.014 0.001 TYR N 50 ARG 0.013 0.000 ARG J 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 66) link_NAG-ASN : angle 2.03557 ( 198) link_ALPHA1-6 : bond 0.00311 ( 3) link_ALPHA1-6 : angle 1.68471 ( 9) link_BETA1-4 : bond 0.00458 ( 18) link_BETA1-4 : angle 1.51357 ( 54) link_ALPHA1-3 : bond 0.01100 ( 3) link_ALPHA1-3 : angle 2.01750 ( 9) hydrogen bonds : bond 0.03766 ( 839) hydrogen bonds : angle 4.86827 ( 2370) SS BOND : bond 0.00393 ( 41) SS BOND : angle 0.68269 ( 82) covalent geometry : bond 0.00265 (22080) covalent geometry : angle 0.54792 (30002) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.6797 (ttmm) cc_final: 0.6530 (tppt) REVERT: I 70 SER cc_start: 0.8412 (t) cc_final: 0.8094 (m) REVERT: A 74 CYS cc_start: 0.7186 (p) cc_final: 0.6882 (t) REVERT: A 110 SER cc_start: 0.8925 (t) cc_final: 0.8620 (m) REVERT: A 430 ILE cc_start: 0.9020 (mm) cc_final: 0.8764 (tp) REVERT: L 17 ASP cc_start: 0.6823 (OUTLIER) cc_final: 0.5868 (m-30) REVERT: M 27 ASP cc_start: 0.6099 (t70) cc_final: 0.5291 (t0) REVERT: M 32 ASN cc_start: 0.7844 (m-40) cc_final: 0.7324 (m-40) REVERT: M 89 LYS cc_start: 0.7855 (tptp) cc_final: 0.7418 (tptp) REVERT: M 108 ARG cc_start: 0.4393 (ptt180) cc_final: 0.4099 (ptt180) REVERT: E 588 ARG cc_start: 0.8093 (ttt90) cc_final: 0.7802 (ttt-90) REVERT: E 634 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7488 (tm-30) REVERT: K 92 ASN cc_start: 0.8151 (p0) cc_final: 0.7288 (t0) REVERT: N 5 VAL cc_start: 0.7279 (p) cc_final: 0.7058 (t) REVERT: N 33 ASN cc_start: 0.8384 (t0) cc_final: 0.8160 (t0) REVERT: N 43 LYS cc_start: 0.7408 (mtmt) cc_final: 0.5991 (mtpp) REVERT: D 150 MET cc_start: 0.8463 (mmm) cc_final: 0.8109 (mmm) outliers start: 40 outliers final: 34 residues processed: 343 average time/residue: 0.3508 time to fit residues: 180.0857 Evaluate side-chains 334 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 299 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 71 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 241 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 181 optimal weight: 0.0170 chunk 211 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 overall best weight: 1.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN B 658 GLN L 3 GLN C 103 GLN K 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.096131 restraints weight = 37584.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.098774 restraints weight = 21409.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100455 restraints weight = 14890.700| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22211 Z= 0.129 Angle : 0.584 13.026 30354 Z= 0.290 Chirality : 0.046 0.303 3615 Planarity : 0.004 0.045 3706 Dihedral : 5.710 55.436 4652 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.88 % Allowed : 12.37 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.60 (0.17), residues: 2544 helix: 1.82 (0.27), residues: 421 sheet: 0.71 (0.18), residues: 814 loop : -0.22 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 94 HIS 0.003 0.001 HIS C 374 PHE 0.012 0.001 PHE I 100C TYR 0.018 0.001 TYR N 99 ARG 0.010 0.000 ARG J 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 66) link_NAG-ASN : angle 1.99290 ( 198) link_ALPHA1-6 : bond 0.00272 ( 3) link_ALPHA1-6 : angle 1.64518 ( 9) link_BETA1-4 : bond 0.00448 ( 18) link_BETA1-4 : angle 1.49694 ( 54) link_ALPHA1-3 : bond 0.01092 ( 3) link_ALPHA1-3 : angle 2.05848 ( 9) hydrogen bonds : bond 0.03766 ( 839) hydrogen bonds : angle 4.84338 ( 2370) SS BOND : bond 0.00302 ( 41) SS BOND : angle 0.74801 ( 82) covalent geometry : bond 0.00299 (22080) covalent geometry : angle 0.55832 (30002) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 307 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 92 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (m110) REVERT: G 103 LYS cc_start: 0.6750 (ttmm) cc_final: 0.6489 (tppt) REVERT: I 70 SER cc_start: 0.8439 (t) cc_final: 0.8115 (m) REVERT: A 74 CYS cc_start: 0.7145 (p) cc_final: 0.6887 (t) REVERT: A 110 SER cc_start: 0.8919 (t) cc_final: 0.8623 (m) REVERT: A 430 ILE cc_start: 0.9004 (mm) cc_final: 0.8756 (tp) REVERT: L 17 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.5906 (m-30) REVERT: M 13 ARG cc_start: 0.5544 (mmp-170) cc_final: 0.5343 (mmp-170) REVERT: M 27 ASP cc_start: 0.6020 (t70) cc_final: 0.5299 (t0) REVERT: M 32 ASN cc_start: 0.7891 (m-40) cc_final: 0.7420 (m-40) REVERT: M 89 LYS cc_start: 0.7849 (tptp) cc_final: 0.7419 (tptp) REVERT: M 108 ARG cc_start: 0.4415 (ptt180) cc_final: 0.4125 (ptt180) REVERT: E 588 ARG cc_start: 0.8150 (ttt90) cc_final: 0.7848 (ttt-90) REVERT: E 634 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7235 (tm-30) REVERT: K 92 ASN cc_start: 0.8110 (p0) cc_final: 0.7202 (t0) REVERT: K 93 ASP cc_start: 0.7501 (p0) cc_final: 0.6792 (p0) REVERT: N 3 GLN cc_start: 0.7680 (pm20) cc_final: 0.7397 (pm20) REVERT: N 5 VAL cc_start: 0.7285 (p) cc_final: 0.7066 (t) REVERT: N 43 LYS cc_start: 0.7311 (mtmt) cc_final: 0.5953 (mtpp) REVERT: D 150 MET cc_start: 0.8438 (mmm) cc_final: 0.8115 (mmm) outliers start: 43 outliers final: 35 residues processed: 331 average time/residue: 0.3615 time to fit residues: 180.1327 Evaluate side-chains 331 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 294 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 31 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 236 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN N 33 ASN F 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.114519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092917 restraints weight = 37491.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095459 restraints weight = 21771.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.097067 restraints weight = 15363.245| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22211 Z= 0.271 Angle : 0.711 9.783 30354 Z= 0.353 Chirality : 0.050 0.336 3615 Planarity : 0.005 0.066 3706 Dihedral : 6.472 58.462 4652 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.84 % Allowed : 12.59 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.24 (0.16), residues: 2544 helix: 1.47 (0.27), residues: 416 sheet: 0.52 (0.18), residues: 802 loop : -0.44 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 94 HIS 0.006 0.001 HIS D 374 PHE 0.018 0.002 PHE A 361 TYR 0.029 0.002 TYR N 99 ARG 0.009 0.001 ARG J 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 66) link_NAG-ASN : angle 2.31242 ( 198) link_ALPHA1-6 : bond 0.00180 ( 3) link_ALPHA1-6 : angle 1.85968 ( 9) link_BETA1-4 : bond 0.00486 ( 18) link_BETA1-4 : angle 1.88003 ( 54) link_ALPHA1-3 : bond 0.00876 ( 3) link_ALPHA1-3 : angle 2.46151 ( 9) hydrogen bonds : bond 0.04735 ( 839) hydrogen bonds : angle 5.20740 ( 2370) SS BOND : bond 0.00423 ( 41) SS BOND : angle 0.98440 ( 82) covalent geometry : bond 0.00659 (22080) covalent geometry : angle 0.68110 (30002) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.6823 (ttmm) cc_final: 0.6372 (ttmt) REVERT: I 58 ARG cc_start: 0.7336 (mtm180) cc_final: 0.7105 (mtm180) REVERT: A 110 SER cc_start: 0.9045 (t) cc_final: 0.8689 (m) REVERT: A 430 ILE cc_start: 0.9002 (mm) cc_final: 0.8784 (tp) REVERT: M 13 ARG cc_start: 0.5822 (mmp-170) cc_final: 0.5572 (mmp-170) REVERT: M 27 ASP cc_start: 0.6122 (t70) cc_final: 0.5334 (t0) REVERT: M 32 ASN cc_start: 0.7946 (m-40) cc_final: 0.7516 (m-40) REVERT: E 634 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7583 (tm-30) REVERT: K 93 ASP cc_start: 0.7653 (p0) cc_final: 0.7217 (p0) REVERT: N 5 VAL cc_start: 0.7374 (p) cc_final: 0.7139 (t) REVERT: N 43 LYS cc_start: 0.7368 (mtmt) cc_final: 0.6123 (mtpp) outliers start: 42 outliers final: 41 residues processed: 307 average time/residue: 0.3818 time to fit residues: 175.4116 Evaluate side-chains 316 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 612 SER Chi-restraints excluded: chain E residue 613 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 81 LYS Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 171 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 129 optimal weight: 0.0770 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 238 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN I 77 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 30 ASN C 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096916 restraints weight = 37287.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099565 restraints weight = 21340.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101251 restraints weight = 14918.717| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 22211 Z= 0.109 Angle : 0.590 8.434 30354 Z= 0.296 Chirality : 0.046 0.283 3615 Planarity : 0.004 0.063 3706 Dihedral : 5.803 57.297 4652 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.14 % Allowed : 13.81 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.45 (0.17), residues: 2544 helix: 1.71 (0.27), residues: 423 sheet: 0.62 (0.18), residues: 821 loop : -0.35 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 94 HIS 0.003 0.001 HIS C 374 PHE 0.013 0.001 PHE I 100C TYR 0.018 0.001 TYR N 99 ARG 0.010 0.000 ARG M 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 66) link_NAG-ASN : angle 2.00401 ( 198) link_ALPHA1-6 : bond 0.00334 ( 3) link_ALPHA1-6 : angle 1.64604 ( 9) link_BETA1-4 : bond 0.00436 ( 18) link_BETA1-4 : angle 1.49977 ( 54) link_ALPHA1-3 : bond 0.01018 ( 3) link_ALPHA1-3 : angle 1.84381 ( 9) hydrogen bonds : bond 0.03725 ( 839) hydrogen bonds : angle 4.85801 ( 2370) SS BOND : bond 0.00278 ( 41) SS BOND : angle 0.72051 ( 82) covalent geometry : bond 0.00244 (22080) covalent geometry : angle 0.56405 (30002) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5088 Ramachandran restraints generated. 2544 Oldfield, 0 Emsley, 2544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 307 time to evaluate : 2.575 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 103 LYS cc_start: 0.6688 (ttmm) cc_final: 0.6352 (ttmt) REVERT: I 58 ARG cc_start: 0.7180 (mtm180) cc_final: 0.6891 (mtm180) REVERT: I 70 SER cc_start: 0.8348 (t) cc_final: 0.8007 (m) REVERT: A 110 SER cc_start: 0.8893 (t) cc_final: 0.8604 (m) REVERT: A 430 ILE cc_start: 0.9043 (mm) cc_final: 0.8823 (tp) REVERT: M 13 ARG cc_start: 0.5669 (mmp-170) cc_final: 0.5447 (mmp-170) REVERT: M 27 ASP cc_start: 0.6106 (t70) cc_final: 0.5359 (t0) REVERT: M 32 ASN cc_start: 0.7839 (m-40) cc_final: 0.7367 (m-40) REVERT: M 89 LYS cc_start: 0.7865 (tptp) cc_final: 0.7479 (tptp) REVERT: M 100 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8581 (ttmt) REVERT: M 108 ARG cc_start: 0.4387 (ptt180) cc_final: 0.4151 (tpp80) REVERT: E 588 ARG cc_start: 0.8151 (ttt90) cc_final: 0.7887 (ttt-90) REVERT: E 634 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7254 (tm-30) REVERT: K 93 ASP cc_start: 0.7857 (p0) cc_final: 0.7530 (p0) REVERT: N 43 LYS cc_start: 0.7230 (mtmt) cc_final: 0.6013 (mtpp) outliers start: 26 outliers final: 24 residues processed: 319 average time/residue: 0.3987 time to fit residues: 189.0027 Evaluate side-chains 320 residues out of total 2288 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 92 ASN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain F residue 595 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 239 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 92 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 30 ASN C 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.115948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094282 restraints weight = 37590.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096864 restraints weight = 21664.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098515 restraints weight = 15237.449| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22211 Z= 0.201 Angle : 0.646 12.266 30354 Z= 0.320 Chirality : 0.048 0.315 3615 Planarity : 0.004 0.062 3706 Dihedral : 6.035 57.870 4652 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.27 % Allowed : 14.07 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.17), residues: 2544 helix: 1.60 (0.27), residues: 423 sheet: 0.53 (0.18), residues: 807 loop : -0.44 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 94 HIS 0.006 0.001 HIS G 89 PHE 0.014 0.002 PHE I 100C TYR 0.022 0.002 TYR N 99 ARG 0.010 0.001 ARG M 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 66) link_NAG-ASN : angle 2.08999 ( 198) link_ALPHA1-6 : bond 0.00240 ( 3) link_ALPHA1-6 : angle 1.70533 ( 9) link_BETA1-4 : bond 0.00442 ( 18) link_BETA1-4 : angle 1.64774 ( 54) link_ALPHA1-3 : bond 0.00883 ( 3) link_ALPHA1-3 : angle 2.13036 ( 9) hydrogen bonds : bond 0.04212 ( 839) hydrogen bonds : angle 4.99725 ( 2370) SS BOND : bond 0.00349 ( 41) SS BOND : angle 0.84693 ( 82) covalent geometry : bond 0.00486 (22080) covalent geometry : angle 0.61986 (30002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7340.94 seconds wall clock time: 128 minutes 2.49 seconds (7682.49 seconds total)