Starting phenix.real_space_refine on Thu Feb 5 20:31:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auh_43880/02_2026/9auh_43880.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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 135 5.16 5 C 12666 2.51 5 N 3354 2.21 5 O 4157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" 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: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 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: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.97, per 1000 atoms: 0.24 Number of scatterers: 20312 At special positions: 0 Unit cell: (150.12, 155.52, 159.84, 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 135 16.00 O 4157 8.00 N 3354 7.00 C 12666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " 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 ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 197 " " NAG B 601 " - " ASN B 386 " " NAG B 602 " - " ASN B 392 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 362 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 88 " " NAG B 607 " - " ASN B 241 " " NAG B 608 " - " ASN B 448 " " NAG B 609 " - " ASN B 442 " " NAG B 610 " - " ASN B 197 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 362 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 442 " " NAG C 610 " - " ASN C 197 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN B 262 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 300 " " NAG T 1 " - " ASN B 156 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 300 " " NAG X 1 " - " ASN C 156 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 940.4 milliseconds 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 48 sheets defined 18.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.659A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.028A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.375A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.705A pdb=" N ALA C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 61' Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.971A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.737A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.827A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 138 " --> pdb=" O GLY C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 138' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.514A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'D' and resid 512 through 516 removed outlier: 4.063A pdb=" N ILE D 515 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 516' Processing helix chain 'D' and resid 530 through 535 removed outlier: 4.023A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.711A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 4.069A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.822A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.602A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.681A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 removed outlier: 3.796A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.937A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.670A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 664 removed outlier: 3.775A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.138A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.589A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 664 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.785A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.978A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.604A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.559A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.941A pdb=" N GLU K 85 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.078A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.087A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.324A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.632A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.709A pdb=" N GLU A 466 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.011A pdb=" N CYS A 378 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.747A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.649A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.629A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB9, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.863A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 434 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.299A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 393 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.105A pdb=" N CYS B 378 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 294 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 309 Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 498 removed outlier: 4.835A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.500A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.797A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.568A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.537A pdb=" N LYS C 155 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AD1, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'C' and resid 259 through 260 removed outlier: 4.038A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.577A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS C 378 " --> pdb=" O GLU C 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.577A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 358 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 393 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD5, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.043A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.358A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.549A pdb=" N THR H 124 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.630A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.604A pdb=" N THR I 124 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.604A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.766A pdb=" N GLY K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.766A pdb=" N GLY K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.599A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.599A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 650 hydrogen bonds defined for protein. 1725 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: 3.79 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5822 1.33 - 1.47: 5799 1.47 - 1.60: 8922 1.60 - 1.73: 0 1.73 - 1.86: 183 Bond restraints: 20726 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.331 1.394 -0.062 7.90e-03 1.60e+04 6.21e+01 bond pdb=" C1 NAG C 603 " pdb=" O5 NAG C 603 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C1 NAG B 603 " pdb=" O5 NAG B 603 " ideal model delta sigma weight residual 1.406 1.500 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C2 MAN N 5 " pdb=" O2 MAN N 5 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C1 MAN N 7 " pdb=" C2 MAN N 7 " ideal model delta sigma weight residual 1.526 1.594 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 20721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 27652 2.97 - 5.94: 403 5.94 - 8.92: 85 8.92 - 11.89: 20 11.89 - 14.86: 4 Bond angle restraints: 28164 Sorted by residual: angle pdb=" N VAL C 430 " pdb=" CA VAL C 430 " pdb=" C VAL C 430 " ideal model delta sigma weight residual 113.20 107.70 5.50 9.60e-01 1.09e+00 3.28e+01 angle pdb=" N ASN C 156 " pdb=" CA ASN C 156 " pdb=" CB ASN C 156 " ideal model delta sigma weight residual 110.30 117.95 -7.65 1.54e+00 4.22e-01 2.47e+01 angle pdb=" C LYS C 155 " pdb=" N ASN C 156 " pdb=" CA ASN C 156 " ideal model delta sigma weight residual 120.68 112.32 8.36 1.70e+00 3.46e-01 2.42e+01 angle pdb=" N THR C 257 " pdb=" CA THR C 257 " pdb=" C THR C 257 " ideal model delta sigma weight residual 108.07 101.76 6.31 1.38e+00 5.25e-01 2.09e+01 angle pdb=" C THR C 257 " pdb=" N GLN C 258 " pdb=" CA GLN C 258 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 ... (remaining 28159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 12459 24.39 - 48.78: 756 48.78 - 73.16: 129 73.16 - 97.55: 62 97.55 - 121.94: 50 Dihedral angle restraints: 13456 sinusoidal: 6334 harmonic: 7122 Sorted by residual: dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -13.01 -72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -154.98 68.98 1 1.00e+01 1.00e-02 6.16e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -137.92 51.92 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 13453 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 3273 0.131 - 0.262: 104 0.262 - 0.393: 15 0.393 - 0.524: 5 0.524 - 0.655: 1 Chirality restraints: 3398 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C1 NAG A 609 " pdb=" ND2 ASN A 442 " pdb=" C2 NAG A 609 " pdb=" O5 NAG A 609 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C2 NAG M 1 " pdb=" C1 NAG M 1 " pdb=" C3 NAG M 1 " pdb=" N2 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.38e+00 ... (remaining 3395 not shown) Planarity restraints: 3519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " 0.008 2.00e-02 2.50e+03 8.27e-02 8.55e+01 pdb=" CG ASN C 156 " -0.093 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.097 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " 0.022 2.00e-02 2.50e+03 4.34e-02 1.89e+01 pdb=" CG ASN C 156 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " 0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 205 " 0.058 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO A 206 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.049 5.00e-02 4.00e+02 ... (remaining 3516 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4890 2.80 - 3.32: 16239 3.32 - 3.85: 31988 3.85 - 4.37: 34207 4.37 - 4.90: 62249 Nonbonded interactions: 149573 Sorted by model distance: nonbonded pdb=" OG SER A 185 " pdb=" O THR A 185b" model vdw 2.273 3.040 nonbonded pdb=" O MET B 369 " pdb=" OG1 THR B 373 " model vdw 2.284 3.040 nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR J 5 " pdb=" OG1 THR J 23 " model vdw 2.302 3.040 nonbonded pdb=" OD2 ASP B 325 " pdb=" OH TYR H 33 " model vdw 2.313 3.040 ... (remaining 149568 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'Q' selection = chain 'U' } ncs_group { reference = (chain 'N' and (resid 2 or resid 5 through 9)) selection = (chain 'R' and (resid 1 or resid 4 through 8)) selection = (chain 'V' and (resid 1 or resid 4 through 8)) } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'P' selection = chain 'T' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.620 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.006 0.096 20849 Z= 0.278 Angle : 1.016 22.535 28495 Z= 0.469 Chirality : 0.062 0.655 3398 Planarity : 0.006 0.092 3477 Dihedral : 17.697 121.939 8794 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2451 helix: -0.86 (0.24), residues: 376 sheet: -0.30 (0.20), residues: 711 loop : -2.29 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 72 TYR 0.042 0.002 TYR H 116 PHE 0.038 0.002 PHE B 317 TRP 0.039 0.002 TRP C 45 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00573 (20726) covalent geometry : angle 0.94870 (28164) SS BOND : bond 0.00456 ( 38) SS BOND : angle 1.82388 ( 76) hydrogen bonds : bond 0.22261 ( 622) hydrogen bonds : angle 8.43743 ( 1725) link_ALPHA1-2 : bond 0.00609 ( 4) link_ALPHA1-2 : angle 2.87234 ( 12) link_ALPHA1-3 : bond 0.00359 ( 9) link_ALPHA1-3 : angle 1.54861 ( 27) link_ALPHA1-6 : bond 0.00787 ( 9) link_ALPHA1-6 : angle 1.76380 ( 27) link_BETA1-4 : bond 0.00800 ( 21) link_BETA1-4 : angle 2.33885 ( 63) link_NAG-ASN : bond 0.00960 ( 42) link_NAG-ASN : angle 5.03336 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LEU cc_start: 0.8126 (tp) cc_final: 0.7751 (tp) REVERT: B 424 ILE cc_start: 0.9433 (mm) cc_final: 0.9231 (mm) REVERT: C 475 MET cc_start: 0.7859 (mmt) cc_final: 0.7499 (mmt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1450 time to fit residues: 72.9366 Evaluate side-chains 266 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 67 ASN A 195 ASN D 607 ASN F 656 ASN G 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132447 restraints weight = 27068.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131535 restraints weight = 37329.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132561 restraints weight = 35176.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132219 restraints weight = 29253.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132600 restraints weight = 28643.944| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20849 Z= 0.230 Angle : 0.781 18.101 28495 Z= 0.374 Chirality : 0.053 0.513 3398 Planarity : 0.005 0.081 3477 Dihedral : 13.610 112.050 4390 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.78 % Allowed : 9.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.17), residues: 2451 helix: 0.19 (0.27), residues: 392 sheet: -0.18 (0.21), residues: 683 loop : -2.24 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.014 0.002 TYR A 223 PHE 0.020 0.002 PHE B 376 TRP 0.026 0.002 TRP E 596 HIS 0.008 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00551 (20726) covalent geometry : angle 0.72611 (28164) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.57676 ( 76) hydrogen bonds : bond 0.04803 ( 622) hydrogen bonds : angle 5.70187 ( 1725) link_ALPHA1-2 : bond 0.00652 ( 4) link_ALPHA1-2 : angle 3.07139 ( 12) link_ALPHA1-3 : bond 0.00985 ( 9) link_ALPHA1-3 : angle 1.95938 ( 27) link_ALPHA1-6 : bond 0.00783 ( 9) link_ALPHA1-6 : angle 1.82676 ( 27) link_BETA1-4 : bond 0.00563 ( 21) link_BETA1-4 : angle 2.33509 ( 63) link_NAG-ASN : bond 0.00751 ( 42) link_NAG-ASN : angle 3.66683 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8702 (mt) cc_final: 0.8499 (mt) REVERT: B 342 LEU cc_start: 0.8302 (tp) cc_final: 0.7895 (tp) REVERT: C 160 ASN cc_start: 0.7871 (t0) cc_final: 0.7068 (p0) REVERT: C 180 ASP cc_start: 0.8581 (t0) cc_final: 0.8336 (t70) REVERT: D 627 THR cc_start: 0.7743 (p) cc_final: 0.7512 (p) REVERT: E 632 ASP cc_start: 0.7751 (t70) cc_final: 0.7286 (t0) REVERT: F 585 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7785 (mtp85) outliers start: 38 outliers final: 28 residues processed: 302 average time/residue: 0.1324 time to fit residues: 63.5441 Evaluate side-chains 282 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN A 302 ASN B 343 GLN C 67 ASN F 630 GLN F 656 ASN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132884 restraints weight = 26843.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131880 restraints weight = 37510.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133063 restraints weight = 36218.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132869 restraints weight = 26870.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133250 restraints weight = 27647.489| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20849 Z= 0.187 Angle : 0.720 17.461 28495 Z= 0.341 Chirality : 0.050 0.465 3398 Planarity : 0.004 0.077 3477 Dihedral : 12.298 107.566 4390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.35 % Allowed : 13.76 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.17), residues: 2451 helix: 0.64 (0.28), residues: 391 sheet: -0.17 (0.20), residues: 693 loop : -2.23 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.016 0.001 TYR L 51 PHE 0.024 0.002 PHE E 522 TRP 0.021 0.001 TRP D 596 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00443 (20726) covalent geometry : angle 0.66476 (28164) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.34861 ( 76) hydrogen bonds : bond 0.04255 ( 622) hydrogen bonds : angle 5.26671 ( 1725) link_ALPHA1-2 : bond 0.00540 ( 4) link_ALPHA1-2 : angle 3.00881 ( 12) link_ALPHA1-3 : bond 0.00958 ( 9) link_ALPHA1-3 : angle 1.66873 ( 27) link_ALPHA1-6 : bond 0.00641 ( 9) link_ALPHA1-6 : angle 1.83194 ( 27) link_BETA1-4 : bond 0.00519 ( 21) link_BETA1-4 : angle 2.00519 ( 63) link_NAG-ASN : bond 0.00810 ( 42) link_NAG-ASN : angle 3.60968 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LEU cc_start: 0.8304 (tp) cc_final: 0.7824 (tp) REVERT: C 154 MET cc_start: 0.8790 (mtp) cc_final: 0.8250 (mtp) REVERT: C 160 ASN cc_start: 0.7943 (t0) cc_final: 0.7181 (p0) REVERT: C 180 ASP cc_start: 0.8518 (t0) cc_final: 0.8280 (t70) REVERT: D 627 THR cc_start: 0.7845 (p) cc_final: 0.7570 (p) REVERT: E 535 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: F 585 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7816 (mtp85) REVERT: H 12 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7755 (mmmt) outliers start: 50 outliers final: 33 residues processed: 311 average time/residue: 0.1386 time to fit residues: 68.0481 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain K residue 40 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 144 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN C 67 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131291 restraints weight = 26795.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.130337 restraints weight = 37373.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131637 restraints weight = 35746.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.131046 restraints weight = 26947.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131643 restraints weight = 27615.568| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20849 Z= 0.181 Angle : 0.701 17.090 28495 Z= 0.332 Chirality : 0.050 0.459 3398 Planarity : 0.004 0.075 3477 Dihedral : 11.440 101.930 4390 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.96 % Allowed : 14.74 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2451 helix: 0.83 (0.29), residues: 391 sheet: -0.22 (0.20), residues: 719 loop : -2.24 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.016 0.001 TYR L 51 PHE 0.022 0.002 PHE E 522 TRP 0.019 0.001 TRP D 596 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00433 (20726) covalent geometry : angle 0.64737 (28164) SS BOND : bond 0.00357 ( 38) SS BOND : angle 1.34835 ( 76) hydrogen bonds : bond 0.04008 ( 622) hydrogen bonds : angle 5.03240 ( 1725) link_ALPHA1-2 : bond 0.00618 ( 4) link_ALPHA1-2 : angle 3.32004 ( 12) link_ALPHA1-3 : bond 0.00967 ( 9) link_ALPHA1-3 : angle 1.74491 ( 27) link_ALPHA1-6 : bond 0.00711 ( 9) link_ALPHA1-6 : angle 1.83513 ( 27) link_BETA1-4 : bond 0.00509 ( 21) link_BETA1-4 : angle 1.85693 ( 63) link_NAG-ASN : bond 0.00781 ( 42) link_NAG-ASN : angle 3.49064 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8112 (t-100) cc_final: 0.7686 (t-100) REVERT: B 342 LEU cc_start: 0.8285 (tp) cc_final: 0.7852 (tp) REVERT: C 154 MET cc_start: 0.8813 (mtp) cc_final: 0.8277 (mtp) REVERT: C 160 ASN cc_start: 0.7953 (t0) cc_final: 0.7185 (p0) REVERT: C 180 ASP cc_start: 0.8479 (t0) cc_final: 0.8260 (t70) REVERT: C 268 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8113 (mtmt) REVERT: D 627 THR cc_start: 0.7871 (p) cc_final: 0.7592 (p) REVERT: F 585 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7869 (mtp85) REVERT: H 12 LYS cc_start: 0.7986 (mmtp) cc_final: 0.7746 (mmmt) REVERT: L 37 TRP cc_start: 0.8454 (m100) cc_final: 0.8124 (m100) outliers start: 63 outliers final: 46 residues processed: 317 average time/residue: 0.1346 time to fit residues: 67.7066 Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 40 GLN Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN B 478 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129147 restraints weight = 26726.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128806 restraints weight = 31682.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129805 restraints weight = 30672.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130045 restraints weight = 23932.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.130257 restraints weight = 22879.926| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20849 Z= 0.140 Angle : 0.668 16.880 28495 Z= 0.314 Chirality : 0.048 0.451 3398 Planarity : 0.004 0.069 3477 Dihedral : 10.751 98.912 4390 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.96 % Allowed : 16.24 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2451 helix: 1.04 (0.29), residues: 389 sheet: -0.28 (0.20), residues: 737 loop : -2.18 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.011 0.001 TYR J 51 PHE 0.022 0.001 PHE E 522 TRP 0.018 0.001 TRP D 596 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00325 (20726) covalent geometry : angle 0.61617 (28164) SS BOND : bond 0.00320 ( 38) SS BOND : angle 1.33163 ( 76) hydrogen bonds : bond 0.03599 ( 622) hydrogen bonds : angle 4.86875 ( 1725) link_ALPHA1-2 : bond 0.00627 ( 4) link_ALPHA1-2 : angle 3.41224 ( 12) link_ALPHA1-3 : bond 0.00991 ( 9) link_ALPHA1-3 : angle 1.76610 ( 27) link_ALPHA1-6 : bond 0.00783 ( 9) link_ALPHA1-6 : angle 1.80343 ( 27) link_BETA1-4 : bond 0.00488 ( 21) link_BETA1-4 : angle 1.67503 ( 63) link_NAG-ASN : bond 0.00727 ( 42) link_NAG-ASN : angle 3.33914 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8073 (t-100) cc_final: 0.7722 (t-100) REVERT: B 342 LEU cc_start: 0.8223 (tp) cc_final: 0.7769 (tp) REVERT: C 122 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7894 (mp) REVERT: C 154 MET cc_start: 0.8851 (mtp) cc_final: 0.8348 (mtp) REVERT: C 317 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.7712 (p90) REVERT: D 522 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4249 (t80) REVERT: D 627 THR cc_start: 0.7833 (p) cc_final: 0.7614 (p) REVERT: H 12 LYS cc_start: 0.8072 (mmtp) cc_final: 0.7822 (mmmt) REVERT: L 37 TRP cc_start: 0.8471 (m100) cc_final: 0.8085 (m100) outliers start: 63 outliers final: 45 residues processed: 318 average time/residue: 0.1423 time to fit residues: 71.2578 Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 271 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 230 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN A 425 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132961 restraints weight = 26473.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.132021 restraints weight = 37255.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133259 restraints weight = 36151.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133231 restraints weight = 28170.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133504 restraints weight = 27836.580| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20849 Z= 0.125 Angle : 0.653 16.606 28495 Z= 0.306 Chirality : 0.047 0.444 3398 Planarity : 0.004 0.071 3477 Dihedral : 10.076 94.766 4390 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 3.10 % Allowed : 16.81 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.17), residues: 2451 helix: 1.22 (0.29), residues: 389 sheet: -0.28 (0.19), residues: 753 loop : -2.14 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 87 TYR 0.010 0.001 TYR B 318 PHE 0.022 0.001 PHE E 522 TRP 0.016 0.001 TRP D 596 HIS 0.007 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00287 (20726) covalent geometry : angle 0.60430 (28164) SS BOND : bond 0.00288 ( 38) SS BOND : angle 1.15027 ( 76) hydrogen bonds : bond 0.03355 ( 622) hydrogen bonds : angle 4.69598 ( 1725) link_ALPHA1-2 : bond 0.00886 ( 4) link_ALPHA1-2 : angle 3.39474 ( 12) link_ALPHA1-3 : bond 0.00997 ( 9) link_ALPHA1-3 : angle 1.77552 ( 27) link_ALPHA1-6 : bond 0.00820 ( 9) link_ALPHA1-6 : angle 1.74720 ( 27) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 1.53682 ( 63) link_NAG-ASN : bond 0.00696 ( 42) link_NAG-ASN : angle 3.23998 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 284 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7540 (t0) cc_final: 0.7312 (t0) REVERT: A 259 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8434 (mp) REVERT: B 112 TRP cc_start: 0.7998 (t-100) cc_final: 0.7664 (t-100) REVERT: C 154 MET cc_start: 0.8841 (mtp) cc_final: 0.8339 (mtp) REVERT: C 317 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.7680 (p90) REVERT: D 522 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.4134 (t80) REVERT: D 627 THR cc_start: 0.7986 (p) cc_final: 0.7608 (p) REVERT: H 12 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7734 (mmmt) REVERT: L 37 TRP cc_start: 0.8444 (m100) cc_final: 0.8061 (m100) outliers start: 66 outliers final: 47 residues processed: 329 average time/residue: 0.1271 time to fit residues: 66.6658 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 271 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 210 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.0050 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 119 GLN H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.152544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126272 restraints weight = 26785.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125349 restraints weight = 41668.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.126290 restraints weight = 37304.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.125830 restraints weight = 30803.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126283 restraints weight = 30438.937| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 20849 Z= 0.264 Angle : 0.791 17.052 28495 Z= 0.376 Chirality : 0.052 0.555 3398 Planarity : 0.005 0.086 3477 Dihedral : 10.423 100.415 4390 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.62 % Allowed : 17.14 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2451 helix: 0.83 (0.28), residues: 392 sheet: -0.24 (0.20), residues: 704 loop : -2.29 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 273 TYR 0.016 0.002 TYR B 217 PHE 0.024 0.002 PHE E 522 TRP 0.023 0.002 TRP A 69 HIS 0.007 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00640 (20726) covalent geometry : angle 0.73786 (28164) SS BOND : bond 0.00416 ( 38) SS BOND : angle 1.69519 ( 76) hydrogen bonds : bond 0.04556 ( 622) hydrogen bonds : angle 4.91432 ( 1725) link_ALPHA1-2 : bond 0.00505 ( 4) link_ALPHA1-2 : angle 3.99269 ( 12) link_ALPHA1-3 : bond 0.00949 ( 9) link_ALPHA1-3 : angle 1.84851 ( 27) link_ALPHA1-6 : bond 0.00638 ( 9) link_ALPHA1-6 : angle 1.91776 ( 27) link_BETA1-4 : bond 0.00573 ( 21) link_BETA1-4 : angle 1.78362 ( 63) link_NAG-ASN : bond 0.00813 ( 42) link_NAG-ASN : angle 3.68063 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7728 (t0) cc_final: 0.7475 (t0) REVERT: A 317 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7724 (p90) REVERT: B 112 TRP cc_start: 0.8132 (t-100) cc_final: 0.7752 (t-100) REVERT: B 342 LEU cc_start: 0.8517 (tp) cc_final: 0.8280 (tp) REVERT: C 154 MET cc_start: 0.8845 (mtp) cc_final: 0.8605 (mtp) REVERT: C 180 ASP cc_start: 0.8526 (t0) cc_final: 0.8097 (t0) REVERT: C 317 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.7953 (p90) REVERT: D 522 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.4720 (t80) REVERT: D 627 THR cc_start: 0.8047 (p) cc_final: 0.7807 (p) REVERT: E 616 ASN cc_start: 0.6842 (m-40) cc_final: 0.6630 (m-40) REVERT: H 12 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7719 (mmmt) REVERT: L 37 TRP cc_start: 0.8501 (m100) cc_final: 0.8110 (m100) outliers start: 77 outliers final: 54 residues processed: 336 average time/residue: 0.1290 time to fit residues: 69.2364 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 93 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131394 restraints weight = 26593.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131116 restraints weight = 34600.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131582 restraints weight = 33349.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131387 restraints weight = 26782.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131795 restraints weight = 26281.738| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20849 Z= 0.158 Angle : 0.704 16.970 28495 Z= 0.331 Chirality : 0.049 0.468 3398 Planarity : 0.004 0.072 3477 Dihedral : 9.880 91.869 4390 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.00 % Allowed : 18.36 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.17), residues: 2451 helix: 1.05 (0.29), residues: 392 sheet: -0.19 (0.20), residues: 706 loop : -2.20 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.012 0.001 TYR J 51 PHE 0.022 0.002 PHE E 522 TRP 0.017 0.001 TRP D 596 HIS 0.013 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00374 (20726) covalent geometry : angle 0.65004 (28164) SS BOND : bond 0.00326 ( 38) SS BOND : angle 1.42067 ( 76) hydrogen bonds : bond 0.03739 ( 622) hydrogen bonds : angle 4.75958 ( 1725) link_ALPHA1-2 : bond 0.00969 ( 4) link_ALPHA1-2 : angle 3.70393 ( 12) link_ALPHA1-3 : bond 0.00980 ( 9) link_ALPHA1-3 : angle 1.79985 ( 27) link_ALPHA1-6 : bond 0.00756 ( 9) link_ALPHA1-6 : angle 1.79332 ( 27) link_BETA1-4 : bond 0.00486 ( 21) link_BETA1-4 : angle 1.62309 ( 63) link_NAG-ASN : bond 0.00740 ( 42) link_NAG-ASN : angle 3.50499 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.6715 (m90) cc_final: 0.6484 (m-70) REVERT: A 317 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7707 (p90) REVERT: B 47 GLU cc_start: 0.6200 (mm-30) cc_final: 0.5914 (mm-30) REVERT: B 112 TRP cc_start: 0.8099 (t-100) cc_final: 0.7779 (t-100) REVERT: B 342 LEU cc_start: 0.8395 (tp) cc_final: 0.8161 (tp) REVERT: B 449 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7862 (mt) REVERT: C 111 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8390 (tt) REVERT: C 154 MET cc_start: 0.8857 (mtp) cc_final: 0.8224 (mtp) REVERT: C 180 ASP cc_start: 0.8535 (t0) cc_final: 0.8240 (t70) REVERT: C 317 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.7686 (p90) REVERT: C 424 ILE cc_start: 0.8910 (mm) cc_final: 0.8571 (mm) REVERT: D 522 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.4783 (t80) REVERT: D 627 THR cc_start: 0.7948 (p) cc_final: 0.7691 (p) REVERT: H 12 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7677 (mmmt) REVERT: I 54 ASN cc_start: 0.8582 (m-40) cc_final: 0.8220 (m-40) REVERT: L 37 TRP cc_start: 0.8405 (m100) cc_final: 0.8068 (m100) outliers start: 64 outliers final: 52 residues processed: 333 average time/residue: 0.1312 time to fit residues: 69.2912 Evaluate side-chains 335 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 8 optimal weight: 0.7980 chunk 229 optimal weight: 0.8980 chunk 206 optimal weight: 0.7980 chunk 159 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 0.0050 chunk 197 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 213 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN F 656 ASN G 119 GLN H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.148988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118857 restraints weight = 27329.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117508 restraints weight = 33605.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118596 restraints weight = 36355.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118755 restraints weight = 27066.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119570 restraints weight = 27234.105| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20849 Z= 0.121 Angle : 0.660 15.762 28495 Z= 0.311 Chirality : 0.047 0.420 3398 Planarity : 0.004 0.064 3477 Dihedral : 9.175 78.372 4390 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.68 % Allowed : 18.83 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.17), residues: 2451 helix: 1.18 (0.29), residues: 400 sheet: -0.04 (0.20), residues: 695 loop : -2.04 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.012 0.001 TYR J 51 PHE 0.021 0.001 PHE E 522 TRP 0.014 0.001 TRP F 631 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00276 (20726) covalent geometry : angle 0.61057 (28164) SS BOND : bond 0.00298 ( 38) SS BOND : angle 1.25071 ( 76) hydrogen bonds : bond 0.03229 ( 622) hydrogen bonds : angle 4.60099 ( 1725) link_ALPHA1-2 : bond 0.00969 ( 4) link_ALPHA1-2 : angle 3.39896 ( 12) link_ALPHA1-3 : bond 0.00946 ( 9) link_ALPHA1-3 : angle 1.80488 ( 27) link_ALPHA1-6 : bond 0.00811 ( 9) link_ALPHA1-6 : angle 1.67050 ( 27) link_BETA1-4 : bond 0.00462 ( 21) link_BETA1-4 : angle 1.45941 ( 63) link_NAG-ASN : bond 0.00695 ( 42) link_NAG-ASN : angle 3.29777 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 292 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8053 (t-100) cc_final: 0.7709 (t-100) REVERT: B 342 LEU cc_start: 0.8223 (tp) cc_final: 0.7981 (tp) REVERT: C 111 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 154 MET cc_start: 0.8832 (mtp) cc_final: 0.8342 (mtp) REVERT: C 180 ASP cc_start: 0.8436 (t0) cc_final: 0.8190 (t70) REVERT: C 317 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7657 (p90) REVERT: C 424 ILE cc_start: 0.8988 (mm) cc_final: 0.8658 (mm) REVERT: D 522 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4760 (t80) REVERT: D 590 GLN cc_start: 0.8013 (tp40) cc_final: 0.7746 (tp40) REVERT: G 89 ASP cc_start: 0.8020 (t70) cc_final: 0.7788 (t0) REVERT: H 12 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7749 (mmmt) REVERT: I 54 ASN cc_start: 0.8403 (m-40) cc_final: 0.7939 (m-40) REVERT: L 37 TRP cc_start: 0.8426 (m100) cc_final: 0.7965 (m100) outliers start: 57 outliers final: 45 residues processed: 330 average time/residue: 0.1326 time to fit residues: 69.3549 Evaluate side-chains 325 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 213 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 overall best weight: 1.5022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.148244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117767 restraints weight = 27487.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116464 restraints weight = 35984.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117944 restraints weight = 35878.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.118020 restraints weight = 25975.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118232 restraints weight = 25904.620| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20849 Z= 0.192 Angle : 0.714 16.597 28495 Z= 0.340 Chirality : 0.049 0.442 3398 Planarity : 0.004 0.076 3477 Dihedral : 9.058 71.790 4390 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.58 % Allowed : 18.97 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.17), residues: 2451 helix: 1.01 (0.28), residues: 402 sheet: -0.09 (0.20), residues: 704 loop : -2.09 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.016 0.001 TYR G 116 PHE 0.022 0.002 PHE E 522 TRP 0.019 0.001 TRP A 69 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00462 (20726) covalent geometry : angle 0.66273 (28164) SS BOND : bond 0.00336 ( 38) SS BOND : angle 1.51509 ( 76) hydrogen bonds : bond 0.03778 ( 622) hydrogen bonds : angle 4.66493 ( 1725) link_ALPHA1-2 : bond 0.00678 ( 4) link_ALPHA1-2 : angle 3.56240 ( 12) link_ALPHA1-3 : bond 0.00883 ( 9) link_ALPHA1-3 : angle 1.77518 ( 27) link_ALPHA1-6 : bond 0.00715 ( 9) link_ALPHA1-6 : angle 1.77324 ( 27) link_BETA1-4 : bond 0.00493 ( 21) link_BETA1-4 : angle 1.54692 ( 63) link_NAG-ASN : bond 0.00779 ( 42) link_NAG-ASN : angle 3.45383 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8060 (t-100) cc_final: 0.7745 (t-100) REVERT: B 342 LEU cc_start: 0.8375 (tp) cc_final: 0.8158 (tp) REVERT: C 111 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8380 (tt) REVERT: C 154 MET cc_start: 0.8821 (mtp) cc_final: 0.8564 (mtp) REVERT: C 180 ASP cc_start: 0.8546 (t0) cc_final: 0.8227 (t70) REVERT: C 317 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7730 (p90) REVERT: C 424 ILE cc_start: 0.8913 (mm) cc_final: 0.8575 (mm) REVERT: D 522 PHE cc_start: 0.6217 (OUTLIER) cc_final: 0.4816 (t80) REVERT: G 89 ASP cc_start: 0.8087 (t70) cc_final: 0.7874 (t0) REVERT: G 90 ASP cc_start: 0.8317 (m-30) cc_final: 0.8095 (m-30) REVERT: H 12 LYS cc_start: 0.8069 (mmtp) cc_final: 0.7813 (mmmt) REVERT: H 29 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7422 (p90) REVERT: L 37 TRP cc_start: 0.8464 (m100) cc_final: 0.7928 (m100) outliers start: 55 outliers final: 47 residues processed: 317 average time/residue: 0.1323 time to fit residues: 66.3460 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 272 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 523 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 147 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 230 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 209 optimal weight: 10.0000 overall best weight: 0.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.148607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.117938 restraints weight = 27388.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116506 restraints weight = 33905.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117804 restraints weight = 35431.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117957 restraints weight = 26629.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118135 restraints weight = 26570.144| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20849 Z= 0.145 Angle : 0.676 16.340 28495 Z= 0.321 Chirality : 0.048 0.431 3398 Planarity : 0.004 0.068 3477 Dihedral : 8.701 68.792 4390 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.58 % Allowed : 19.15 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.17), residues: 2451 helix: 1.32 (0.29), residues: 390 sheet: -0.10 (0.20), residues: 705 loop : -2.04 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.015 0.001 TYR G 116 PHE 0.022 0.001 PHE E 522 TRP 0.014 0.001 TRP F 596 HIS 0.003 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00343 (20726) covalent geometry : angle 0.62670 (28164) SS BOND : bond 0.00306 ( 38) SS BOND : angle 1.31986 ( 76) hydrogen bonds : bond 0.03458 ( 622) hydrogen bonds : angle 4.59016 ( 1725) link_ALPHA1-2 : bond 0.00724 ( 4) link_ALPHA1-2 : angle 3.27003 ( 12) link_ALPHA1-3 : bond 0.00907 ( 9) link_ALPHA1-3 : angle 1.76367 ( 27) link_ALPHA1-6 : bond 0.00792 ( 9) link_ALPHA1-6 : angle 1.68381 ( 27) link_BETA1-4 : bond 0.00475 ( 21) link_BETA1-4 : angle 1.48263 ( 63) link_NAG-ASN : bond 0.00713 ( 42) link_NAG-ASN : angle 3.35424 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.05 seconds wall clock time: 53 minutes 34.90 seconds (3214.90 seconds total)