Starting phenix.real_space_refine on Tue Jun 17 18:48:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auh_43880/06_2025/9auh_43880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auh_43880/06_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_43880/06_2025/9auh_43880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auh_43880/06_2025/9auh_43880.map" model { file = "/net/cci-nas-00/data/ceres_data/9auh_43880/06_2025/9auh_43880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auh_43880/06_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-5710/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: 12.31, per 1000 atoms: 0.61 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: 5.11 Conformation dependent library (CDL) restraints added in 2.3 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: 2.58 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: 6.74 Time building geometry restraints manager: 6.07 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.220 Process input model: 45.420 Find NCS groups from input model: 0.790 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.070 ------------------------------------------------------------------------------- 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 : 2.130 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: 0.2937 time to fit residues: 147.3469 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 : 2.160 ------------------------------------------------------------------------------- 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 = 33818.840| |-----------------------------------------------------------------------------| 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 : 2.053 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: 0.8284 (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: 0.2967 time to fit residues: 142.0659 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 : 1.997 ------------------------------------------------------------------------------- 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: 3.9990 chunk 55 optimal weight: 2.9990 chunk 198 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 104 optimal weight: 0.0980 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128505 restraints weight = 26827.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127754 restraints weight = 35240.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128484 restraints weight = 34653.264| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 20849 Z= 0.320 Angle : 0.852 17.486 28495 Z= 0.409 Chirality : 0.055 0.460 3398 Planarity : 0.005 0.091 3477 Dihedral : 12.608 109.429 4390 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.68 % Allowed : 13.94 % Favored : 83.38 % 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: -1.88 (0.17), residues: 2451 helix: 0.36 (0.28), residues: 393 sheet: -0.33 (0.20), residues: 726 loop : -2.39 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 596 HIS 0.013 0.002 HIS K 41 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 0.00866 ( 42) link_NAG-ASN : angle 3.91101 ( 126) link_ALPHA1-6 : bond 0.00631 ( 9) link_ALPHA1-6 : angle 1.96331 ( 27) link_BETA1-4 : bond 0.00633 ( 21) link_BETA1-4 : angle 2.18096 ( 63) link_ALPHA1-2 : bond 0.00716 ( 4) link_ALPHA1-2 : angle 3.31515 ( 12) link_ALPHA1-3 : bond 0.00936 ( 9) link_ALPHA1-3 : angle 1.78591 ( 27) hydrogen bonds : bond 0.05265 ( 622) hydrogen bonds : angle 5.37500 ( 1725) SS BOND : bond 0.00478 ( 38) SS BOND : angle 1.71789 ( 76) covalent geometry : bond 0.00776 (20726) covalent geometry : angle 0.79703 (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 349 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 292 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 259 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8462 (mp) REVERT: B 342 LEU cc_start: 0.8422 (tp) cc_final: 0.8060 (tp) REVERT: C 180 ASP cc_start: 0.8564 (t0) cc_final: 0.8344 (t70) REVERT: C 317 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.7906 (p90) REVERT: D 627 THR cc_start: 0.7960 (p) cc_final: 0.7692 (p) REVERT: E 632 ASP cc_start: 0.7776 (t70) cc_final: 0.7347 (t0) outliers start: 57 outliers final: 39 residues processed: 332 average time/residue: 0.3111 time to fit residues: 161.4993 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 : 2.025 ------------------------------------------------------------------------------- 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 11 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain 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: 0.6980 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 217 optimal weight: 0.0170 chunk 129 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN B 478 ASN C 67 ASN ** D 653 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128796 restraints weight = 26604.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128756 restraints weight = 32722.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129724 restraints weight = 30526.846| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 0.048 20849 Z= 0.126 Angle : 0.669 16.993 28495 Z= 0.316 Chirality : 0.048 0.446 3398 Planarity : 0.004 0.067 3477 Dihedral : 11.396 105.517 4390 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.68 % Allowed : 15.54 % Favored : 81.78 % 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: -1.53 (0.17), residues: 2451 helix: 0.95 (0.29), residues: 389 sheet: -0.11 (0.20), residues: 689 loop : -2.20 (0.16), residues: 1373 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 0.021 0.001 PHE E 522 TYR 0.011 0.001 TYR L 51 ARG 0.003 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 42) link_NAG-ASN : angle 3.43950 ( 126) link_ALPHA1-6 : bond 0.00772 ( 9) link_ALPHA1-6 : angle 1.78796 ( 27) link_BETA1-4 : bond 0.00487 ( 21) link_BETA1-4 : angle 1.78898 ( 63) link_ALPHA1-2 : bond 0.00752 ( 4) link_ALPHA1-2 : angle 3.05177 ( 12) link_ALPHA1-3 : bond 0.01012 ( 9) link_ALPHA1-3 : angle 1.74578 ( 27) hydrogen bonds : bond 0.03639 ( 622) hydrogen bonds : angle 4.98945 ( 1725) SS BOND : bond 0.00364 ( 38) SS BOND : angle 1.26375 ( 76) covalent geometry : bond 0.00286 (20726) covalent geometry : angle 0.61558 (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 343 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 2.030 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: 0.8115 (t-100) cc_final: 0.7821 (t-100) REVERT: B 167 ASP cc_start: 0.7969 (m-30) cc_final: 0.7749 (m-30) REVERT: B 342 LEU cc_start: 0.8315 (tp) cc_final: 0.7810 (tp) REVERT: C 122 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (mp) REVERT: C 160 ASN cc_start: 0.7950 (t0) cc_final: 0.7218 (p0) REVERT: C 424 ILE cc_start: 0.8889 (mm) cc_final: 0.8535 (mm) REVERT: D 522 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.4462 (t80) REVERT: D 627 THR cc_start: 0.7841 (p) cc_final: 0.7619 (p) REVERT: E 530 MET cc_start: 0.7508 (mtt) cc_final: 0.7298 (mtt) REVERT: E 652 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7248 (mt0) REVERT: L 37 TRP cc_start: 0.8460 (m100) cc_final: 0.8106 (m100) outliers start: 57 outliers final: 30 residues processed: 319 average time/residue: 0.2921 time to fit residues: 147.5784 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 2.284 ------------------------------------------------------------------------------- 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 111 LEU Chi-restraints excluded: chain C residue 122 LEU 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 522 PHE 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 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 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: 2.9990 chunk 26 optimal weight: 2.9990 chunk 161 optimal weight: 0.0670 chunk 180 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 235 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 221 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 119 GLN ** H 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 = 0.3738 r_free = 0.3738 target = 0.156156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129420 restraints weight = 27024.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.128357 restraints weight = 38319.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129241 restraints weight = 36089.400| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20849 Z= 0.159 Angle : 0.678 16.945 28495 Z= 0.320 Chirality : 0.049 0.443 3398 Planarity : 0.004 0.069 3477 Dihedral : 10.871 107.763 4390 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 3.05 % Allowed : 16.71 % Favored : 80.23 % 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: -1.49 (0.17), residues: 2451 helix: 1.07 (0.29), residues: 390 sheet: -0.19 (0.20), residues: 701 loop : -2.16 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 596 HIS 0.004 0.001 HIS B 374 PHE 0.022 0.001 PHE E 522 TYR 0.011 0.001 TYR B 318 ARG 0.004 0.000 ARG B 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 42) link_NAG-ASN : angle 3.40167 ( 126) link_ALPHA1-6 : bond 0.00753 ( 9) link_ALPHA1-6 : angle 1.81929 ( 27) link_BETA1-4 : bond 0.00493 ( 21) link_BETA1-4 : angle 1.64522 ( 63) link_ALPHA1-2 : bond 0.00759 ( 4) link_ALPHA1-2 : angle 3.14780 ( 12) link_ALPHA1-3 : bond 0.00993 ( 9) link_ALPHA1-3 : angle 1.74759 ( 27) hydrogen bonds : bond 0.03724 ( 622) hydrogen bonds : angle 4.86074 ( 1725) SS BOND : bond 0.00350 ( 38) SS BOND : angle 1.34604 ( 76) covalent geometry : bond 0.00378 (20726) covalent geometry : angle 0.62641 (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 344 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 279 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8064 (t-100) cc_final: 0.7767 (t-100) REVERT: B 342 LEU cc_start: 0.8326 (tp) cc_final: 0.7868 (tp) REVERT: C 122 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7936 (mp) REVERT: C 424 ILE cc_start: 0.9010 (mm) cc_final: 0.8658 (mm) REVERT: D 522 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.4464 (t80) REVERT: D 627 THR cc_start: 0.7951 (p) cc_final: 0.7572 (p) REVERT: E 530 MET cc_start: 0.7611 (mtt) cc_final: 0.7404 (mtt) REVERT: E 616 ASN cc_start: 0.6789 (m-40) cc_final: 0.6583 (m-40) REVERT: L 37 TRP cc_start: 0.8438 (m100) cc_final: 0.8025 (m100) outliers start: 65 outliers final: 47 residues processed: 322 average time/residue: 0.2997 time to fit residues: 153.5292 Evaluate side-chains 317 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 268 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 161 THR Chi-restraints excluded: chain B residue 209 THR 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 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN 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 122 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 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 618 ASN 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 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 119 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 54 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 146 optimal weight: 0.2980 chunk 217 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 234 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129364 restraints weight = 26919.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128307 restraints weight = 38390.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129055 restraints weight = 35988.040| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20849 Z= 0.141 Angle : 0.668 16.844 28495 Z= 0.314 Chirality : 0.049 0.540 3398 Planarity : 0.004 0.066 3477 Dihedral : 10.434 106.413 4390 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.00 % Allowed : 17.37 % Favored : 79.62 % 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: -1.43 (0.17), residues: 2451 helix: 1.20 (0.29), residues: 389 sheet: -0.17 (0.20), residues: 709 loop : -2.15 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 596 HIS 0.007 0.001 HIS J 41 PHE 0.022 0.001 PHE E 522 TYR 0.010 0.001 TYR C 318 ARG 0.004 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00657 ( 42) link_NAG-ASN : angle 3.33560 ( 126) link_ALPHA1-6 : bond 0.00780 ( 9) link_ALPHA1-6 : angle 1.78980 ( 27) link_BETA1-4 : bond 0.00485 ( 21) link_BETA1-4 : angle 1.57122 ( 63) link_ALPHA1-2 : bond 0.00968 ( 4) link_ALPHA1-2 : angle 3.05889 ( 12) link_ALPHA1-3 : bond 0.00967 ( 9) link_ALPHA1-3 : angle 1.74737 ( 27) hydrogen bonds : bond 0.03491 ( 622) hydrogen bonds : angle 4.75809 ( 1725) SS BOND : bond 0.00321 ( 38) SS BOND : angle 1.39028 ( 76) covalent geometry : bond 0.00332 (20726) covalent geometry : angle 0.61706 (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 350 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 1.992 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: 0.8372 (OUTLIER) cc_final: 0.7344 (p90) REVERT: B 112 TRP cc_start: 0.8066 (t-100) cc_final: 0.7726 (t-100) REVERT: C 122 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7906 (mp) REVERT: C 317 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.7727 (p90) REVERT: D 522 PHE cc_start: 0.5688 (OUTLIER) cc_final: 0.4459 (t80) REVERT: D 627 THR cc_start: 0.7799 (p) cc_final: 0.7529 (p) REVERT: L 37 TRP cc_start: 0.8417 (m100) cc_final: 0.7990 (m100) outliers start: 64 outliers final: 45 residues processed: 326 average time/residue: 0.2929 time to fit residues: 151.6064 Evaluate side-chains 322 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 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 161 THR 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 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 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 593 LEU 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 H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 53 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 15 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 218 optimal weight: 0.0870 chunk 128 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6760 ------------------------------------------------------------------------------- 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 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 = 0.3772 r_free = 0.3772 target = 0.159273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.132576 restraints weight = 26584.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.131747 restraints weight = 35867.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133063 restraints weight = 34939.434| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20849 Z= 0.122 Angle : 0.645 15.793 28495 Z= 0.302 Chirality : 0.047 0.434 3398 Planarity : 0.004 0.064 3477 Dihedral : 9.800 99.106 4390 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.15 % Allowed : 18.31 % 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: -1.33 (0.17), residues: 2451 helix: 1.32 (0.29), residues: 389 sheet: -0.13 (0.20), residues: 706 loop : -2.06 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 596 HIS 0.003 0.001 HIS C 249 PHE 0.021 0.001 PHE E 522 TYR 0.024 0.001 TYR J 51 ARG 0.004 0.000 ARG B 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 42) link_NAG-ASN : angle 3.24867 ( 126) link_ALPHA1-6 : bond 0.00815 ( 9) link_ALPHA1-6 : angle 1.73097 ( 27) link_BETA1-4 : bond 0.00457 ( 21) link_BETA1-4 : angle 1.46131 ( 63) link_ALPHA1-2 : bond 0.01092 ( 4) link_ALPHA1-2 : angle 3.21090 ( 12) link_ALPHA1-3 : bond 0.00964 ( 9) link_ALPHA1-3 : angle 1.79628 ( 27) hydrogen bonds : bond 0.03198 ( 622) hydrogen bonds : angle 4.60036 ( 1725) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.22205 ( 76) covalent geometry : bond 0.00280 (20726) covalent geometry : angle 0.59512 (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 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 286 time to evaluate : 2.008 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 66 HIS cc_start: 0.6688 (m90) cc_final: 0.6457 (m-70) REVERT: A 317 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7689 (p90) REVERT: B 112 TRP cc_start: 0.8028 (t-100) cc_final: 0.7735 (t-100) REVERT: B 342 LEU cc_start: 0.8293 (tp) cc_final: 0.8026 (tp) REVERT: C 122 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7665 (mp) REVERT: C 180 ASP cc_start: 0.8279 (t0) cc_final: 0.7663 (t0) REVERT: C 317 PHE cc_start: 0.8937 (OUTLIER) cc_final: 0.7618 (p90) REVERT: D 522 PHE cc_start: 0.5912 (OUTLIER) cc_final: 0.4718 (t80) REVERT: D 627 THR cc_start: 0.7762 (p) cc_final: 0.7477 (p) REVERT: L 37 TRP cc_start: 0.8439 (m100) cc_final: 0.8049 (m100) outliers start: 67 outliers final: 48 residues processed: 331 average time/residue: 0.2734 time to fit residues: 144.9819 Evaluate side-chains 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 276 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 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 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 B residue 389 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 363 GLN 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 595 ILE 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 62 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 123 optimal weight: 0.7980 chunk 151 optimal weight: 0.0040 chunk 101 optimal weight: 0.0370 chunk 114 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 228 optimal weight: 0.0030 overall best weight: 0.3480 ------------------------------------------------------------------------------- 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 F 656 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.155711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.127259 restraints weight = 27263.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126518 restraints weight = 31608.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127859 restraints weight = 30141.218| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20849 Z= 0.106 Angle : 0.632 16.374 28495 Z= 0.295 Chirality : 0.047 0.444 3398 Planarity : 0.003 0.059 3477 Dihedral : 9.350 98.131 4390 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.63 % Allowed : 19.06 % Favored : 78.31 % 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: -1.21 (0.17), residues: 2451 helix: 1.48 (0.29), residues: 388 sheet: -0.15 (0.20), residues: 743 loop : -1.98 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 631 HIS 0.002 0.001 HIS B 330 PHE 0.021 0.001 PHE E 522 TYR 0.013 0.001 TYR H 80 ARG 0.004 0.000 ARG B 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00660 ( 42) link_NAG-ASN : angle 3.19827 ( 126) link_ALPHA1-6 : bond 0.00871 ( 9) link_ALPHA1-6 : angle 1.65635 ( 27) link_BETA1-4 : bond 0.00458 ( 21) link_BETA1-4 : angle 1.38342 ( 63) link_ALPHA1-2 : bond 0.00942 ( 4) link_ALPHA1-2 : angle 3.34008 ( 12) link_ALPHA1-3 : bond 0.00948 ( 9) link_ALPHA1-3 : angle 1.78393 ( 27) hydrogen bonds : bond 0.02929 ( 622) hydrogen bonds : angle 4.46197 ( 1725) SS BOND : bond 0.00268 ( 38) SS BOND : angle 1.05747 ( 76) covalent geometry : bond 0.00233 (20726) covalent geometry : angle 0.58342 (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 347 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 2.134 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 317 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7787 (p90) REVERT: B 112 TRP cc_start: 0.8020 (t-100) cc_final: 0.7652 (t-100) REVERT: B 342 LEU cc_start: 0.8221 (tp) cc_final: 0.7985 (tp) REVERT: C 180 ASP cc_start: 0.8449 (t0) cc_final: 0.8191 (t70) REVERT: C 424 ILE cc_start: 0.8971 (mm) cc_final: 0.8610 (mm) REVERT: D 522 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.4726 (t80) REVERT: L 37 TRP cc_start: 0.8427 (m100) cc_final: 0.7993 (m100) outliers start: 56 outliers final: 44 residues processed: 328 average time/residue: 0.2906 time to fit residues: 151.8580 Evaluate side-chains 322 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 276 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 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 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 161 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain 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 592 LEU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 62 GLN 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 L residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 119 optimal weight: 0.9980 chunk 204 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 201 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 0.5980 chunk 208 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 76 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 575 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.159785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133720 restraints weight = 26870.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132975 restraints weight = 37838.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134037 restraints weight = 35115.424| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2324 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= 0.115 Angle : 0.642 17.314 28495 Z= 0.299 Chirality : 0.047 0.595 3398 Planarity : 0.004 0.062 3477 Dihedral : 9.066 96.216 4390 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.54 % Allowed : 19.62 % Favored : 77.84 % 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: -1.19 (0.17), residues: 2451 helix: 1.51 (0.29), residues: 387 sheet: -0.12 (0.20), residues: 743 loop : -1.99 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 596 HIS 0.003 0.001 HIS A 374 PHE 0.020 0.001 PHE E 522 TYR 0.015 0.001 TYR H 80 ARG 0.007 0.000 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00691 ( 42) link_NAG-ASN : angle 3.26255 ( 126) link_ALPHA1-6 : bond 0.00838 ( 9) link_ALPHA1-6 : angle 1.61392 ( 27) link_BETA1-4 : bond 0.00467 ( 21) link_BETA1-4 : angle 1.36428 ( 63) link_ALPHA1-2 : bond 0.00750 ( 4) link_ALPHA1-2 : angle 3.42250 ( 12) link_ALPHA1-3 : bond 0.00916 ( 9) link_ALPHA1-3 : angle 1.80191 ( 27) hydrogen bonds : bond 0.02959 ( 622) hydrogen bonds : angle 4.40855 ( 1725) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.07782 ( 76) covalent geometry : bond 0.00262 (20726) covalent geometry : angle 0.59311 (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 341 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 287 time to evaluate : 2.198 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: 0.8426 (OUTLIER) cc_final: 0.8015 (p90) REVERT: B 112 TRP cc_start: 0.7934 (t-100) cc_final: 0.7607 (t-100) REVERT: B 342 LEU cc_start: 0.8244 (tp) cc_final: 0.8004 (tp) REVERT: C 92 ASN cc_start: 0.7937 (m-40) cc_final: 0.7712 (m-40) REVERT: C 180 ASP cc_start: 0.8472 (t0) cc_final: 0.8219 (t70) REVERT: C 424 ILE cc_start: 0.9001 (mm) cc_final: 0.8647 (mm) REVERT: D 522 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.4722 (t80) outliers start: 54 outliers final: 45 residues processed: 326 average time/residue: 0.3299 time to fit residues: 172.8313 Evaluate side-chains 330 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 283 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 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 161 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE 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 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 62 GLN Chi-restraints excluded: chain I residue 71 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: 2.9990 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129917 restraints weight = 26773.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129487 restraints weight = 34752.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.129551 restraints weight = 35650.971| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20849 Z= 0.220 Angle : 0.747 17.389 28495 Z= 0.353 Chirality : 0.051 0.554 3398 Planarity : 0.004 0.078 3477 Dihedral : 9.364 95.722 4390 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.54 % Allowed : 19.20 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.44 (0.17), residues: 2451 helix: 1.14 (0.29), residues: 392 sheet: -0.20 (0.20), residues: 716 loop : -2.13 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 69 HIS 0.007 0.001 HIS B 374 PHE 0.023 0.002 PHE E 522 TYR 0.019 0.002 TYR G 116 ARG 0.007 0.001 ARG E 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00867 ( 42) link_NAG-ASN : angle 3.64285 ( 126) link_ALPHA1-6 : bond 0.00739 ( 9) link_ALPHA1-6 : angle 1.77872 ( 27) link_BETA1-4 : bond 0.00555 ( 21) link_BETA1-4 : angle 1.57135 ( 63) link_ALPHA1-2 : bond 0.00578 ( 4) link_ALPHA1-2 : angle 3.71682 ( 12) link_ALPHA1-3 : bond 0.00941 ( 9) link_ALPHA1-3 : angle 1.79223 ( 27) hydrogen bonds : bond 0.04029 ( 622) hydrogen bonds : angle 4.69296 ( 1725) SS BOND : bond 0.00371 ( 38) SS BOND : angle 1.53600 ( 76) covalent geometry : bond 0.00535 (20726) covalent geometry : angle 0.69383 (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 337 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 2.210 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: 0.8108 (t-100) cc_final: 0.7749 (t-100) REVERT: B 342 LEU cc_start: 0.8518 (tp) cc_final: 0.8293 (tp) REVERT: C 92 ASN cc_start: 0.8053 (m-40) cc_final: 0.7771 (m110) REVERT: C 180 ASP cc_start: 0.8537 (t0) cc_final: 0.8160 (t70) REVERT: C 317 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7726 (p90) REVERT: C 424 ILE cc_start: 0.8952 (mm) cc_final: 0.8602 (mm) REVERT: D 522 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.4832 (t80) REVERT: D 530 MET cc_start: 0.8114 (mmm) cc_final: 0.7549 (mtt) REVERT: D 617 ARG cc_start: 0.7382 (ptm160) cc_final: 0.6979 (ptm160) REVERT: D 621 GLU cc_start: 0.7898 (pp20) cc_final: 0.6918 (pp20) outliers start: 54 outliers final: 40 residues processed: 325 average time/residue: 0.2984 time to fit residues: 152.2326 Evaluate side-chains 318 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 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 161 THR Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 377 ASN Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 622 ILE 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 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 55 SER 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: 1.9990 chunk 171 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 226 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 212 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 106 optimal weight: 0.0970 chunk 176 optimal weight: 6.9990 chunk 188 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120366 restraints weight = 27442.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119370 restraints weight = 34648.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120641 restraints weight = 35322.905| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20849 Z= 0.109 Angle : 0.654 17.229 28495 Z= 0.306 Chirality : 0.047 0.501 3398 Planarity : 0.004 0.056 3477 Dihedral : 8.691 98.775 4390 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.92 % Allowed : 20.33 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.17), residues: 2451 helix: 1.48 (0.29), residues: 389 sheet: -0.10 (0.20), residues: 711 loop : -1.97 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 37 HIS 0.002 0.000 HIS G 35 PHE 0.021 0.001 PHE E 522 TYR 0.014 0.001 TYR J 51 ARG 0.004 0.000 ARG J 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00707 ( 42) link_NAG-ASN : angle 3.29880 ( 126) link_ALPHA1-6 : bond 0.00886 ( 9) link_ALPHA1-6 : angle 1.55835 ( 27) link_BETA1-4 : bond 0.00471 ( 21) link_BETA1-4 : angle 1.40298 ( 63) link_ALPHA1-2 : bond 0.00946 ( 4) link_ALPHA1-2 : angle 3.24950 ( 12) link_ALPHA1-3 : bond 0.00951 ( 9) link_ALPHA1-3 : angle 1.73847 ( 27) hydrogen bonds : bond 0.02995 ( 622) hydrogen bonds : angle 4.46204 ( 1725) SS BOND : bond 0.00311 ( 38) SS BOND : angle 1.13318 ( 76) covalent geometry : bond 0.00244 (20726) covalent geometry : angle 0.60590 (28164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6320.22 seconds wall clock time: 111 minutes 1.70 seconds (6661.70 seconds total)