Starting phenix.real_space_refine on Tue May 20 17:17:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_43880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_43880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_43880.map" model { file = "/net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_43880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auh_43880/05_2025/9auh_43880_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.03, per 1000 atoms: 0.64 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: 5.88 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.77 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: 6.75 Time building geometry restraints manager: 6.70 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: 1.820 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: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 47.160 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (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 TRP 0.039 0.002 TRP C 45 HIS 0.007 0.001 HIS A 66 PHE 0.038 0.002 PHE B 317 TYR 0.042 0.002 TYR H 116 ARG 0.012 0.001 ARG I 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00960 ( 42) link_NAG-ASN : angle 5.03336 ( 126) 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_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) hydrogen bonds : bond 0.22261 ( 622) hydrogen bonds : angle 8.43743 ( 1725) SS BOND : bond 0.00456 ( 38) SS BOND : angle 1.82388 ( 76) covalent geometry : bond 0.00573 (20726) covalent geometry : angle 0.94870 (28164) *********************** 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 : 2.015 Fit side-chains revert: symmetry clash 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: 0.9230 (mm) REVERT: C 475 MET cc_start: 0.7859 (mmt) cc_final: 0.7498 (mmt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2874 time to fit residues: 143.6301 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 : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 207 optimal weight: 4.9990 chunk 186 optimal weight: 0.0270 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 99 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 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 = 0.3768 r_free = 0.3768 target = 0.159031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133421 restraints weight = 26909.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132908 restraints weight = 35690.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133934 restraints weight = 33818.848| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20849 Z= 0.157 Angle : 0.713 18.400 28495 Z= 0.339 Chirality : 0.050 0.464 3398 Planarity : 0.004 0.072 3477 Dihedral : 14.031 111.442 4390 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 1.27 % Allowed : 8.64 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2451 helix: 0.41 (0.28), residues: 382 sheet: -0.11 (0.21), residues: 684 loop : -2.16 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 596 HIS 0.005 0.001 HIS B 374 PHE 0.019 0.002 PHE E 522 TYR 0.010 0.001 TYR L 38 ARG 0.005 0.000 ARG C 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 42) link_NAG-ASN : angle 3.48148 ( 126) link_ALPHA1-6 : bond 0.00853 ( 9) link_ALPHA1-6 : angle 1.79132 ( 27) link_BETA1-4 : bond 0.00529 ( 21) link_BETA1-4 : angle 2.12197 ( 63) link_ALPHA1-2 : bond 0.00726 ( 4) link_ALPHA1-2 : angle 2.92408 ( 12) link_ALPHA1-3 : bond 0.01080 ( 9) link_ALPHA1-3 : angle 1.93280 ( 27) hydrogen bonds : bond 0.04436 ( 622) hydrogen bonds : angle 5.79394 ( 1725) SS BOND : bond 0.00367 ( 38) SS BOND : angle 1.33086 ( 76) covalent geometry : bond 0.00364 (20726) covalent geometry : angle 0.65914 (28164) *********************** 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 315 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 288 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 342 LEU cc_start: 0.8129 (tp) cc_final: 0.7713 (tp) REVERT: B 424 ILE cc_start: 0.9409 (mm) cc_final: 0.9063 (mm) REVERT: C 160 ASN cc_start: 0.7878 (t0) cc_final: 0.7093 (p0) REVERT: C 180 ASP cc_start: 0.8515 (t0) cc_final: 0.8283 (t70) REVERT: D 627 THR cc_start: 0.7625 (p) cc_final: 0.7384 (p) outliers start: 27 outliers final: 20 residues processed: 303 average time/residue: 0.3037 time to fit residues: 144.6012 Evaluate side-chains 288 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 75 SER 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 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 114 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 104 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 656 ASN G 6 GLN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.154040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128720 restraints weight = 26790.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128046 restraints weight = 34736.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127931 restraints weight = 34071.247| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 20849 Z= 0.297 Angle : 0.836 17.349 28495 Z= 0.402 Chirality : 0.054 0.463 3398 Planarity : 0.005 0.089 3477 Dihedral : 12.490 108.088 4390 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 2.91 % Allowed : 13.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.17), residues: 2451 helix: 0.41 (0.28), residues: 393 sheet: -0.28 (0.20), residues: 699 loop : -2.32 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 596 HIS 0.011 0.002 HIS B 374 PHE 0.025 0.003 PHE E 522 TYR 0.020 0.002 TYR L 51 ARG 0.007 0.001 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00880 ( 42) link_NAG-ASN : angle 3.87624 ( 126) link_ALPHA1-6 : bond 0.00652 ( 9) link_ALPHA1-6 : angle 1.90362 ( 27) link_BETA1-4 : bond 0.00642 ( 21) link_BETA1-4 : angle 2.13984 ( 63) link_ALPHA1-2 : bond 0.00638 ( 4) link_ALPHA1-2 : angle 2.97806 ( 12) link_ALPHA1-3 : bond 0.00951 ( 9) link_ALPHA1-3 : angle 1.74039 ( 27) hydrogen bonds : bond 0.05210 ( 622) hydrogen bonds : angle 5.32487 ( 1725) SS BOND : bond 0.00441 ( 38) SS BOND : angle 1.76339 ( 76) covalent geometry : bond 0.00725 (20726) covalent geometry : angle 0.78154 (28164) *********************** 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 356 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 2.155 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 225 ILE cc_start: 0.8627 (mt) cc_final: 0.8409 (mt) REVERT: A 259 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8488 (mp) REVERT: B 342 LEU cc_start: 0.8425 (tp) cc_final: 0.8029 (tp) REVERT: C 180 ASP cc_start: 0.8526 (t0) cc_final: 0.8304 (t70) REVERT: C 317 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.7902 (p90) REVERT: D 627 THR cc_start: 0.7953 (p) cc_final: 0.7680 (p) REVERT: E 616 ASN cc_start: 0.6862 (m-40) cc_final: 0.6634 (m-40) REVERT: E 632 ASP cc_start: 0.7820 (t70) cc_final: 0.7406 (t0) outliers start: 62 outliers final: 39 residues processed: 337 average time/residue: 0.3044 time to fit residues: 160.4311 Evaluate side-chains 309 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 268 time to evaluate : 2.442 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 288 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 284 ILE 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 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 321 ASP Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 603 ILE 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 30 THR Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 5 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 71 THR 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 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 28 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 217 optimal weight: 0.0020 chunk 129 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 196 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 656 ASN G 6 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132304 restraints weight = 26853.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131475 restraints weight = 38169.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132711 restraints weight = 36128.295| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20849 Z= 0.119 Angle : 0.659 16.905 28495 Z= 0.311 Chirality : 0.048 0.444 3398 Planarity : 0.004 0.063 3477 Dihedral : 11.157 104.279 4390 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.30 % Allowed : 15.54 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2451 helix: 0.99 (0.29), residues: 389 sheet: -0.16 (0.20), residues: 697 loop : -2.17 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 596 HIS 0.003 0.001 HIS C 330 PHE 0.020 0.001 PHE E 522 TYR 0.010 0.001 TYR L 51 ARG 0.003 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00673 ( 42) link_NAG-ASN : angle 3.33301 ( 126) link_ALPHA1-6 : bond 0.00851 ( 9) link_ALPHA1-6 : angle 1.78094 ( 27) link_BETA1-4 : bond 0.00478 ( 21) link_BETA1-4 : angle 1.73559 ( 63) link_ALPHA1-2 : bond 0.00830 ( 4) link_ALPHA1-2 : angle 2.97955 ( 12) link_ALPHA1-3 : bond 0.00988 ( 9) link_ALPHA1-3 : angle 1.74374 ( 27) hydrogen bonds : bond 0.03469 ( 622) hydrogen bonds : angle 4.93213 ( 1725) SS BOND : bond 0.00321 ( 38) SS BOND : angle 1.24085 ( 76) covalent geometry : bond 0.00266 (20726) covalent geometry : angle 0.60700 (28164) *********************** 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 345 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 296 time to evaluate : 2.486 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: 0.8041 (t-100) cc_final: 0.7684 (t-100) REVERT: B 167 ASP cc_start: 0.7753 (m-30) cc_final: 0.7523 (m-30) REVERT: B 342 LEU cc_start: 0.8262 (tp) cc_final: 0.7695 (tp) REVERT: C 160 ASN cc_start: 0.7864 (t0) cc_final: 0.7135 (p0) REVERT: C 424 ILE cc_start: 0.8896 (mm) cc_final: 0.8530 (mm) REVERT: D 627 THR cc_start: 0.7651 (p) cc_final: 0.7431 (p) REVERT: L 37 TRP cc_start: 0.8350 (m100) cc_final: 0.8046 (m100) outliers start: 49 outliers final: 30 residues processed: 326 average time/residue: 0.2959 time to fit residues: 154.5915 Evaluate side-chains 305 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 275 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 207 LYS 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 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 248 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 111 LEU Chi-restraints excluded: chain C residue 202 THR 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 630 GLN 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 H residue 11 VAL Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP 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 121 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 180 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 225 optimal weight: 5.9990 chunk 235 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133384 restraints weight = 26674.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132532 restraints weight = 38536.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133821 restraints weight = 35168.860| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1980 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= 0.117 Angle : 0.647 16.825 28495 Z= 0.303 Chirality : 0.048 0.439 3398 Planarity : 0.004 0.063 3477 Dihedral : 10.448 98.681 4390 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.58 % Allowed : 16.76 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.17), residues: 2451 helix: 1.22 (0.29), residues: 389 sheet: -0.12 (0.20), residues: 700 loop : -2.10 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 596 HIS 0.011 0.001 HIS J 41 PHE 0.022 0.001 PHE E 522 TYR 0.016 0.001 TYR J 51 ARG 0.003 0.000 ARG H 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00662 ( 42) link_NAG-ASN : angle 3.22209 ( 126) link_ALPHA1-6 : bond 0.00831 ( 9) link_ALPHA1-6 : angle 1.74631 ( 27) link_BETA1-4 : bond 0.00468 ( 21) link_BETA1-4 : angle 1.53637 ( 63) link_ALPHA1-2 : bond 0.00865 ( 4) link_ALPHA1-2 : angle 3.58812 ( 12) link_ALPHA1-3 : bond 0.01031 ( 9) link_ALPHA1-3 : angle 1.75454 ( 27) hydrogen bonds : bond 0.03279 ( 622) hydrogen bonds : angle 4.75161 ( 1725) SS BOND : bond 0.00314 ( 38) SS BOND : angle 1.23570 ( 76) covalent geometry : bond 0.00266 (20726) covalent geometry : angle 0.59674 (28164) *********************** 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 350 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.7983 (t-100) cc_final: 0.7647 (t-100) REVERT: C 180 ASP cc_start: 0.8462 (t0) cc_final: 0.8005 (t0) REVERT: C 424 ILE cc_start: 0.9038 (mm) cc_final: 0.8717 (mm) REVERT: D 522 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.4494 (t80) REVERT: D 627 THR cc_start: 0.7910 (p) cc_final: 0.7523 (p) REVERT: G 70 MET cc_start: 0.8634 (mtt) cc_final: 0.8426 (mtm) REVERT: L 37 TRP cc_start: 0.8410 (m100) cc_final: 0.8009 (m100) outliers start: 55 outliers final: 35 residues processed: 328 average time/residue: 0.2967 time to fit residues: 154.2643 Evaluate side-chains 314 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 2.109 ------------------------------------------------------------------------------- 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 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 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 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 323 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 632 ASP 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 71 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 54 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 173 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 ** 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 = 0.3729 r_free = 0.3729 target = 0.155401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130037 restraints weight = 26654.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129720 restraints weight = 33882.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.130137 restraints weight = 34165.241| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20849 Z= 0.211 Angle : 0.727 15.991 28495 Z= 0.345 Chirality : 0.050 0.461 3398 Planarity : 0.004 0.077 3477 Dihedral : 10.425 99.760 4390 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.43 % Allowed : 17.37 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2451 helix: 0.99 (0.29), residues: 392 sheet: -0.19 (0.20), residues: 709 loop : -2.22 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 69 HIS 0.007 0.001 HIS B 374 PHE 0.023 0.002 PHE E 522 TYR 0.015 0.002 TYR L 51 ARG 0.005 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 42) link_NAG-ASN : angle 3.45551 ( 126) link_ALPHA1-6 : bond 0.00705 ( 9) link_ALPHA1-6 : angle 1.85729 ( 27) link_BETA1-4 : bond 0.00518 ( 21) link_BETA1-4 : angle 1.63878 ( 63) link_ALPHA1-2 : bond 0.00917 ( 4) link_ALPHA1-2 : angle 3.66620 ( 12) link_ALPHA1-3 : bond 0.00981 ( 9) link_ALPHA1-3 : angle 1.88976 ( 27) hydrogen bonds : bond 0.04018 ( 622) hydrogen bonds : angle 4.81507 ( 1725) SS BOND : bond 0.00384 ( 38) SS BOND : angle 1.59881 ( 76) covalent geometry : bond 0.00509 (20726) covalent geometry : angle 0.67574 (28164) *********************** 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 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 280 time to evaluate : 2.266 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 317 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7428 (p90) REVERT: A 417 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7513 (mm-40) REVERT: B 112 TRP cc_start: 0.8058 (t-100) cc_final: 0.7669 (t-100) REVERT: B 342 LEU cc_start: 0.8461 (tp) cc_final: 0.8226 (tp) REVERT: C 180 ASP cc_start: 0.8494 (t0) cc_final: 0.8049 (t0) REVERT: C 317 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.7714 (p90) REVERT: D 522 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.4622 (t80) REVERT: D 627 THR cc_start: 0.7873 (p) cc_final: 0.7630 (p) REVERT: E 616 ASN cc_start: 0.6807 (m-40) cc_final: 0.6594 (m-40) REVERT: L 37 TRP cc_start: 0.8469 (m100) cc_final: 0.7983 (m100) outliers start: 73 outliers final: 47 residues processed: 330 average time/residue: 0.3043 time to fit residues: 157.4945 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 : 2.080 ------------------------------------------------------------------------------- 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 195 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 417 GLN 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 85 VAL 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 323 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 603 ILE 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 592 LEU 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 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 71 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 15 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 chunk 133 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129117 restraints weight = 26771.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128245 restraints weight = 37822.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.129283 restraints weight = 35130.521| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2307 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= 0.197 Angle : 0.718 16.552 28495 Z= 0.338 Chirality : 0.050 0.470 3398 Planarity : 0.004 0.077 3477 Dihedral : 10.284 98.338 4390 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.19 % Allowed : 17.93 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2451 helix: 0.98 (0.29), residues: 392 sheet: -0.19 (0.20), residues: 704 loop : -2.21 (0.16), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 596 HIS 0.006 0.001 HIS B 374 PHE 0.022 0.002 PHE E 522 TYR 0.013 0.001 TYR J 51 ARG 0.006 0.000 ARG B 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00749 ( 42) link_NAG-ASN : angle 3.52250 ( 126) link_ALPHA1-6 : bond 0.00697 ( 9) link_ALPHA1-6 : angle 1.86218 ( 27) link_BETA1-4 : bond 0.00489 ( 21) link_BETA1-4 : angle 1.63707 ( 63) link_ALPHA1-2 : bond 0.00817 ( 4) link_ALPHA1-2 : angle 3.82534 ( 12) link_ALPHA1-3 : bond 0.00947 ( 9) link_ALPHA1-3 : angle 1.85710 ( 27) hydrogen bonds : bond 0.03927 ( 622) hydrogen bonds : angle 4.80081 ( 1725) SS BOND : bond 0.00353 ( 38) SS BOND : angle 1.49193 ( 76) covalent geometry : bond 0.00474 (20726) covalent geometry : angle 0.66416 (28164) *********************** 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 346 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 278 time to evaluate : 2.149 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 317 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7909 (p90) REVERT: B 112 TRP cc_start: 0.8090 (t-100) cc_final: 0.7765 (t-100) REVERT: B 342 LEU cc_start: 0.8418 (tp) cc_final: 0.8188 (tp) REVERT: B 449 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7959 (mt) REVERT: C 180 ASP cc_start: 0.8549 (t0) cc_final: 0.8207 (t70) REVERT: C 317 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.7729 (p90) REVERT: D 522 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.4649 (t80) REVERT: D 627 THR cc_start: 0.7975 (p) cc_final: 0.7700 (p) REVERT: E 616 ASN cc_start: 0.6828 (m-40) cc_final: 0.6619 (m-40) REVERT: L 37 TRP cc_start: 0.8439 (m100) cc_final: 0.8082 (m100) outliers start: 68 outliers final: 49 residues processed: 327 average time/residue: 0.3028 time to fit residues: 155.8089 Evaluate side-chains 324 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 2.023 ------------------------------------------------------------------------------- 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 274 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 ILE 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 201 CYS 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 85 VAL 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 323 ILE 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 592 LEU 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 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 29 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain K residue 48 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 123 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 228 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 H 6 GLN ** 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 = 0.3699 r_free = 0.3699 target = 0.152662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122397 restraints weight = 27311.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121632 restraints weight = 35217.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.122755 restraints weight = 34037.658| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2310 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= 0.124 Angle : 0.663 17.616 28495 Z= 0.310 Chirality : 0.048 0.611 3398 Planarity : 0.004 0.065 3477 Dihedral : 9.643 87.936 4390 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.58 % Allowed : 18.73 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2451 helix: 1.25 (0.29), residues: 390 sheet: -0.09 (0.20), residues: 703 loop : -2.09 (0.16), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 631 HIS 0.003 0.001 HIS A 66 PHE 0.022 0.001 PHE E 522 TYR 0.013 0.001 TYR J 51 ARG 0.006 0.000 ARG B 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00737 ( 42) link_NAG-ASN : angle 3.48671 ( 126) link_ALPHA1-6 : bond 0.00798 ( 9) link_ALPHA1-6 : angle 1.73073 ( 27) link_BETA1-4 : bond 0.00453 ( 21) link_BETA1-4 : angle 1.49733 ( 63) link_ALPHA1-2 : bond 0.00762 ( 4) link_ALPHA1-2 : angle 3.38851 ( 12) link_ALPHA1-3 : bond 0.00892 ( 9) link_ALPHA1-3 : angle 1.75566 ( 27) hydrogen bonds : bond 0.03237 ( 622) hydrogen bonds : angle 4.63721 ( 1725) SS BOND : bond 0.00299 ( 38) SS BOND : angle 1.21306 ( 76) covalent geometry : bond 0.00283 (20726) covalent geometry : angle 0.60846 (28164) *********************** 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 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7966 (p90) REVERT: B 112 TRP cc_start: 0.8097 (t-100) cc_final: 0.7783 (t-100) REVERT: B 342 LEU cc_start: 0.8262 (tp) cc_final: 0.8037 (tp) REVERT: B 449 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7832 (mt) REVERT: C 180 ASP cc_start: 0.8466 (t0) cc_final: 0.8069 (t70) REVERT: C 424 ILE cc_start: 0.8982 (mm) cc_final: 0.8652 (mm) REVERT: D 522 PHE cc_start: 0.6118 (OUTLIER) cc_final: 0.4871 (t80) REVERT: D 627 THR cc_start: 0.7911 (p) cc_final: 0.7676 (p) REVERT: G 38 ARG cc_start: 0.8022 (tmm-80) cc_final: 0.7805 (tmm-80) REVERT: L 37 TRP cc_start: 0.8436 (m100) cc_final: 0.7984 (m100) outliers start: 55 outliers final: 43 residues processed: 324 average time/residue: 0.2907 time to fit residues: 148.4300 Evaluate side-chains 321 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 275 time to evaluate : 2.055 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 294 ILE 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 125 LEU Chi-restraints excluded: chain B residue 201 CYS 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 389 ASN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 85 VAL 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 323 ILE Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 522 PHE 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 592 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS 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 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 119 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 190 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** E 575 GLN G 119 GLN H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN K 71 ASN L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.129717 restraints weight = 26941.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128680 restraints weight = 38815.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129946 restraints weight = 35682.405| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 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 : 0.004 0.042 20849 Z= 0.147 Angle : 0.679 17.339 28495 Z= 0.319 Chirality : 0.048 0.530 3398 Planarity : 0.004 0.068 3477 Dihedral : 9.479 87.563 4390 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.00 % Allowed : 18.45 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2451 helix: 1.25 (0.29), residues: 390 sheet: -0.11 (0.20), residues: 704 loop : -2.07 (0.16), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 117 HIS 0.004 0.001 HIS B 374 PHE 0.022 0.001 PHE E 522 TYR 0.013 0.001 TYR H 80 ARG 0.008 0.000 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 42) link_NAG-ASN : angle 3.48696 ( 126) link_ALPHA1-6 : bond 0.00758 ( 9) link_ALPHA1-6 : angle 1.71574 ( 27) link_BETA1-4 : bond 0.00474 ( 21) link_BETA1-4 : angle 1.49120 ( 63) link_ALPHA1-2 : bond 0.00600 ( 4) link_ALPHA1-2 : angle 3.60382 ( 12) link_ALPHA1-3 : bond 0.00906 ( 9) link_ALPHA1-3 : angle 1.78390 ( 27) hydrogen bonds : bond 0.03417 ( 622) hydrogen bonds : angle 4.60482 ( 1725) SS BOND : bond 0.00336 ( 38) SS BOND : angle 1.35290 ( 76) covalent geometry : bond 0.00348 (20726) covalent geometry : angle 0.62557 (28164) *********************** 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 340 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.8176 (p90) REVERT: B 112 TRP cc_start: 0.8077 (t-100) cc_final: 0.7729 (t-100) REVERT: B 342 LEU cc_start: 0.8328 (tp) cc_final: 0.8106 (tp) REVERT: B 449 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7852 (mt) REVERT: C 180 ASP cc_start: 0.8454 (t0) cc_final: 0.8073 (t70) REVERT: C 424 ILE cc_start: 0.9005 (mm) cc_final: 0.8687 (mm) REVERT: D 522 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.4883 (t80) REVERT: D 627 THR cc_start: 0.7957 (p) cc_final: 0.7608 (p) REVERT: G 38 ARG cc_start: 0.8054 (tmm-80) cc_final: 0.7836 (tmm-80) REVERT: H 29 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7247 (p90) REVERT: L 37 TRP cc_start: 0.8445 (m100) cc_final: 0.8006 (m100) outliers start: 64 outliers final: 52 residues processed: 322 average time/residue: 0.3157 time to fit residues: 162.9518 Evaluate side-chains 329 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 273 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 195 ASN Chi-restraints excluded: chain A residue 274 SER 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 125 LEU Chi-restraints excluded: chain B residue 201 CYS 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 389 ASN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 85 VAL 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 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 501 CYS 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 592 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 593 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 121 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 I residue 30 THR Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 105 THR 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 77 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** E 575 GLN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 71 ASN L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127951 restraints weight = 27030.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127249 restraints weight = 38529.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128345 restraints weight = 36179.031| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2525 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= 0.191 Angle : 0.719 17.450 28495 Z= 0.339 Chirality : 0.050 0.525 3398 Planarity : 0.004 0.074 3477 Dihedral : 9.458 82.230 4390 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.63 % Allowed : 18.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2451 helix: 1.14 (0.29), residues: 390 sheet: -0.15 (0.20), residues: 702 loop : -2.12 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 69 HIS 0.005 0.001 HIS B 374 PHE 0.023 0.002 PHE E 522 TYR 0.015 0.001 TYR J 51 ARG 0.005 0.000 ARG B 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 42) link_NAG-ASN : angle 3.63798 ( 126) link_ALPHA1-6 : bond 0.00757 ( 9) link_ALPHA1-6 : angle 1.78123 ( 27) link_BETA1-4 : bond 0.00516 ( 21) link_BETA1-4 : angle 1.57853 ( 63) link_ALPHA1-2 : bond 0.00489 ( 4) link_ALPHA1-2 : angle 3.59194 ( 12) link_ALPHA1-3 : bond 0.00923 ( 9) link_ALPHA1-3 : angle 1.75187 ( 27) hydrogen bonds : bond 0.03836 ( 622) hydrogen bonds : angle 4.69112 ( 1725) SS BOND : bond 0.00366 ( 38) SS BOND : angle 1.47422 ( 76) covalent geometry : bond 0.00459 (20726) covalent geometry : angle 0.66382 (28164) ********************** 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 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 285 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8060 (t-100) cc_final: 0.7718 (t-100) REVERT: B 342 LEU cc_start: 0.8445 (tp) cc_final: 0.8235 (tp) REVERT: B 449 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7949 (mt) REVERT: C 180 ASP cc_start: 0.8522 (t0) cc_final: 0.8146 (t70) REVERT: C 317 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7646 (p90) REVERT: C 424 ILE cc_start: 0.8914 (mm) cc_final: 0.8576 (mm) REVERT: D 522 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5003 (t80) REVERT: D 621 GLU cc_start: 0.7924 (pp20) cc_final: 0.6959 (pp20) REVERT: D 627 THR cc_start: 0.7961 (p) cc_final: 0.7625 (p) REVERT: G 38 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7865 (tmm-80) REVERT: H 29 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7419 (p90) REVERT: I 54 ASN cc_start: 0.8574 (m-40) cc_final: 0.8141 (m-40) REVERT: L 37 TRP cc_start: 0.8428 (m100) cc_final: 0.7942 (m100) outliers start: 56 outliers final: 45 residues processed: 327 average time/residue: 0.2982 time to fit residues: 153.1148 Evaluate side-chains 323 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 274 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 274 SER 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 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 201 CYS 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 85 VAL 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 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 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 520 LEU 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 119 GLN Chi-restraints excluded: chain H residue 29 PHE 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 71 THR Chi-restraints excluded: chain J residue 23 THR 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 36 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 212 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 0.0050 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** 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 = 0.3719 r_free = 0.3719 target = 0.154501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127974 restraints weight = 27058.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127151 restraints weight = 39337.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128342 restraints weight = 36349.918| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 20849 Z= 0.211 Angle : 0.875 58.888 28495 Z= 0.448 Chirality : 0.050 0.592 3398 Planarity : 0.004 0.074 3477 Dihedral : 9.458 82.272 4390 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.58 % Allowed : 19.48 % Favored : 77.93 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2451 helix: 1.14 (0.29), residues: 390 sheet: -0.15 (0.20), residues: 702 loop : -2.12 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 596 HIS 0.005 0.001 HIS B 374 PHE 0.023 0.002 PHE E 522 TYR 0.014 0.001 TYR J 51 ARG 0.005 0.000 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.02644 ( 42) link_NAG-ASN : angle 3.84785 ( 126) link_ALPHA1-6 : bond 0.00753 ( 9) link_ALPHA1-6 : angle 1.78118 ( 27) link_BETA1-4 : bond 0.00497 ( 21) link_BETA1-4 : angle 1.58003 ( 63) link_ALPHA1-2 : bond 0.00579 ( 4) link_ALPHA1-2 : angle 3.57728 ( 12) link_ALPHA1-3 : bond 0.00930 ( 9) link_ALPHA1-3 : angle 1.77667 ( 27) hydrogen bonds : bond 0.03777 ( 622) hydrogen bonds : angle 4.69108 ( 1725) SS BOND : bond 0.00346 ( 38) SS BOND : angle 1.73621 ( 76) covalent geometry : bond 0.00470 (20726) covalent geometry : angle 0.82605 (28164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6090.29 seconds wall clock time: 108 minutes 4.20 seconds (6484.20 seconds total)