Starting phenix.real_space_refine on Thu Sep 18 21:18:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9auh_43880/09_2025/9auh_43880_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9auh_43880/09_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_43880/09_2025/9auh_43880.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9auh_43880/09_2025/9auh_43880.map" model { file = "/net/cci-nas-00/data/ceres_data/9auh_43880/09_2025/9auh_43880_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9auh_43880/09_2025/9auh_43880_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 12666 2.51 5 N 3354 2.21 5 O 4157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20312 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "E" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1030 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 989 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 4.65, per 1000 atoms: 0.23 Number of scatterers: 20312 At special positions: 0 Unit cell: (150.12, 155.52, 159.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4157 8.00 N 3354 7.00 C 12666 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN R 4 " - " MAN R 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " MAN R 6 " - " MAN R 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " MAN V 6 " - " MAN V 7 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 6 " " MAN R 6 " - " MAN R 8 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 6 " " MAN V 6 " - " MAN V 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 442 " " NAG A 610 " - " ASN A 197 " " NAG B 601 " - " ASN B 386 " " NAG B 602 " - " ASN B 392 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 362 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 88 " " NAG B 607 " - " ASN B 241 " " NAG B 608 " - " ASN B 448 " " NAG B 609 " - " ASN B 442 " " NAG B 610 " - " ASN B 197 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 362 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 442 " " NAG C 610 " - " ASN C 197 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN B 262 " " NAG R 1 " - " ASN B 332 " " NAG S 1 " - " ASN B 300 " " NAG T 1 " - " ASN B 156 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 300 " " NAG X 1 " - " ASN C 156 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 692.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 48 sheets defined 18.2% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.659A pdb=" N LYS A 63 " --> pdb=" O ALA A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.028A pdb=" N ASP A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 475 through 483 Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.532A pdb=" N ALA B 60 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 98 through 116 removed outlier: 4.375A pdb=" N ASP B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'C' and resid 57 through 61 removed outlier: 3.705A pdb=" N ALA C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 61' Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.971A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.737A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.827A pdb=" N GLY C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY C 138 " --> pdb=" O GLY C 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 134 through 138' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.514A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 475 through 483 Processing helix chain 'D' and resid 512 through 516 removed outlier: 4.063A pdb=" N ILE D 515 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 516 " --> pdb=" O VAL D 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 512 through 516' Processing helix chain 'D' and resid 530 through 535 removed outlier: 4.023A pdb=" N MET D 535 " --> pdb=" O GLY D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.711A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 4.069A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.822A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.602A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 Processing helix chain 'E' and resid 536 through 542 removed outlier: 3.681A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 596 removed outlier: 3.796A pdb=" N ALA E 578 " --> pdb=" O LYS E 574 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG E 579 " --> pdb=" O GLN E 575 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL E 580 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TRP E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 626 removed outlier: 3.937A pdb=" N MET E 626 " --> pdb=" O ILE E 622 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.670A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 639 through 664 removed outlier: 3.775A pdb=" N ASP E 664 " --> pdb=" O LEU E 660 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 570 through 596 removed outlier: 4.138A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.589A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 664 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.785A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.978A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.604A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.559A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU J 85 " --> pdb=" O ALA J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.941A pdb=" N GLU K 85 " --> pdb=" O ALA K 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 85 removed outlier: 4.078A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.087A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.503A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.324A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.632A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.709A pdb=" N GLU A 466 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.011A pdb=" N CYS A 378 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 309 Processing sheet with id=AB2, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.747A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.649A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AB5, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.629A pdb=" N GLY B 237 " --> pdb=" O PHE B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB8, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB9, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.863A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B 434 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.299A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 393 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.105A pdb=" N CYS B 378 " --> pdb=" O GLU B 381 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER B 334 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 294 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 304 through 309 Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 498 removed outlier: 4.835A pdb=" N VAL F 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL C 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N THR F 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR C 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS F 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.500A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 245 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.797A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.568A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 154 through 155 removed outlier: 3.537A pdb=" N LYS C 155 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AD1, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AD2, first strand: chain 'C' and resid 259 through 260 removed outlier: 4.038A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.577A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 421 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS C 378 " --> pdb=" O GLU C 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 271 through 273 removed outlier: 10.577A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.756A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL C 292 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 358 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 393 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD5, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.043A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP G 73 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.358A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.549A pdb=" N THR H 124 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.630A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.604A pdb=" N THR I 124 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TRP I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.604A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AE7, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.766A pdb=" N GLY K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.766A pdb=" N GLY K 12 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF1, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.599A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.599A pdb=" N GLY L 12 " --> pdb=" O THR L 108 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 18 through 23 650 hydrogen bonds defined for protein. 1725 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.52 Time building geometry restraints manager: 2.28 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: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.090 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 20849 Z= 0.278 Angle : 1.016 22.535 28495 Z= 0.469 Chirality : 0.062 0.655 3398 Planarity : 0.006 0.092 3477 Dihedral : 17.697 121.939 8794 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.59 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.16), residues: 2451 helix: -0.86 (0.24), residues: 376 sheet: -0.30 (0.20), residues: 711 loop : -2.29 (0.15), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 72 TYR 0.042 0.002 TYR H 116 PHE 0.038 0.002 PHE B 317 TRP 0.039 0.002 TRP C 45 HIS 0.007 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00573 (20726) covalent geometry : angle 0.94870 (28164) SS BOND : bond 0.00456 ( 38) SS BOND : angle 1.82388 ( 76) hydrogen bonds : bond 0.22261 ( 622) hydrogen bonds : angle 8.43743 ( 1725) link_ALPHA1-2 : bond 0.00609 ( 4) link_ALPHA1-2 : angle 2.87234 ( 12) link_ALPHA1-3 : bond 0.00359 ( 9) link_ALPHA1-3 : angle 1.54861 ( 27) link_ALPHA1-6 : bond 0.00787 ( 9) link_ALPHA1-6 : angle 1.76380 ( 27) link_BETA1-4 : bond 0.00800 ( 21) link_BETA1-4 : angle 2.33885 ( 63) link_NAG-ASN : bond 0.00960 ( 42) link_NAG-ASN : angle 5.03336 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LEU cc_start: 0.8126 (tp) cc_final: 0.7751 (tp) REVERT: B 424 ILE cc_start: 0.9433 (mm) cc_final: 0.9231 (mm) REVERT: C 475 MET cc_start: 0.7859 (mmt) cc_final: 0.7499 (mmt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1345 time to fit residues: 67.4400 Evaluate side-chains 266 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 67 ASN A 195 ASN D 607 ASN F 656 ASN G 119 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.132447 restraints weight = 27068.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.131535 restraints weight = 37329.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132561 restraints weight = 35176.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132219 restraints weight = 29253.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.132600 restraints weight = 28643.944| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20849 Z= 0.230 Angle : 0.781 18.101 28495 Z= 0.374 Chirality : 0.053 0.513 3398 Planarity : 0.005 0.081 3477 Dihedral : 13.610 112.050 4390 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.78 % Allowed : 9.62 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.17), residues: 2451 helix: 0.19 (0.27), residues: 392 sheet: -0.18 (0.21), residues: 683 loop : -2.24 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 273 TYR 0.014 0.002 TYR A 223 PHE 0.020 0.002 PHE B 376 TRP 0.026 0.002 TRP E 596 HIS 0.008 0.002 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00551 (20726) covalent geometry : angle 0.72611 (28164) SS BOND : bond 0.00392 ( 38) SS BOND : angle 1.57676 ( 76) hydrogen bonds : bond 0.04803 ( 622) hydrogen bonds : angle 5.70187 ( 1725) link_ALPHA1-2 : bond 0.00652 ( 4) link_ALPHA1-2 : angle 3.07139 ( 12) link_ALPHA1-3 : bond 0.00985 ( 9) link_ALPHA1-3 : angle 1.95938 ( 27) link_ALPHA1-6 : bond 0.00783 ( 9) link_ALPHA1-6 : angle 1.82676 ( 27) link_BETA1-4 : bond 0.00563 ( 21) link_BETA1-4 : angle 2.33509 ( 63) link_NAG-ASN : bond 0.00751 ( 42) link_NAG-ASN : angle 3.66683 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8702 (mt) cc_final: 0.8500 (mt) REVERT: B 342 LEU cc_start: 0.8302 (tp) cc_final: 0.7895 (tp) REVERT: C 160 ASN cc_start: 0.7870 (t0) cc_final: 0.7068 (p0) REVERT: C 180 ASP cc_start: 0.8581 (t0) cc_final: 0.8336 (t70) REVERT: D 627 THR cc_start: 0.7743 (p) cc_final: 0.7512 (p) REVERT: E 632 ASP cc_start: 0.7751 (t70) cc_final: 0.7286 (t0) REVERT: F 585 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7785 (mtp85) outliers start: 38 outliers final: 28 residues processed: 302 average time/residue: 0.1345 time to fit residues: 64.0434 Evaluate side-chains 282 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 607 ASN Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 164 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 231 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN A 302 ASN B 343 GLN C 67 ASN F 630 GLN F 656 ASN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.158649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132884 restraints weight = 26843.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131880 restraints weight = 37510.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133063 restraints weight = 36218.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.132869 restraints weight = 26870.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.133250 restraints weight = 27647.489| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20849 Z= 0.187 Angle : 0.720 17.461 28495 Z= 0.341 Chirality : 0.050 0.465 3398 Planarity : 0.004 0.077 3477 Dihedral : 12.298 107.566 4390 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.35 % Allowed : 13.76 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.17), residues: 2451 helix: 0.64 (0.28), residues: 391 sheet: -0.17 (0.20), residues: 693 loop : -2.23 (0.16), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.016 0.001 TYR L 51 PHE 0.024 0.002 PHE E 522 TRP 0.021 0.001 TRP D 596 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00443 (20726) covalent geometry : angle 0.66476 (28164) SS BOND : bond 0.00344 ( 38) SS BOND : angle 1.34861 ( 76) hydrogen bonds : bond 0.04255 ( 622) hydrogen bonds : angle 5.26671 ( 1725) link_ALPHA1-2 : bond 0.00540 ( 4) link_ALPHA1-2 : angle 3.00881 ( 12) link_ALPHA1-3 : bond 0.00958 ( 9) link_ALPHA1-3 : angle 1.66873 ( 27) link_ALPHA1-6 : bond 0.00641 ( 9) link_ALPHA1-6 : angle 1.83194 ( 27) link_BETA1-4 : bond 0.00519 ( 21) link_BETA1-4 : angle 2.00519 ( 63) link_NAG-ASN : bond 0.00810 ( 42) link_NAG-ASN : angle 3.60968 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 ILE cc_start: 0.8630 (mt) cc_final: 0.8430 (mt) REVERT: B 342 LEU cc_start: 0.8304 (tp) cc_final: 0.7824 (tp) REVERT: C 154 MET cc_start: 0.8790 (mtp) cc_final: 0.8250 (mtp) REVERT: C 160 ASN cc_start: 0.7943 (t0) cc_final: 0.7181 (p0) REVERT: C 180 ASP cc_start: 0.8518 (t0) cc_final: 0.8280 (t70) REVERT: D 627 THR cc_start: 0.7845 (p) cc_final: 0.7570 (p) REVERT: E 535 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7539 (mpp) REVERT: F 585 ARG cc_start: 0.8104 (ttp80) cc_final: 0.7816 (mtp85) REVERT: H 12 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7755 (mmmt) outliers start: 50 outliers final: 33 residues processed: 311 average time/residue: 0.1399 time to fit residues: 68.8220 Evaluate side-chains 304 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 270 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain K residue 40 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 144 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN C 67 ASN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 119 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.156552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.130419 restraints weight = 26806.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129311 restraints weight = 38305.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130764 restraints weight = 35422.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129701 restraints weight = 27274.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130328 restraints weight = 25954.808| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20849 Z= 0.181 Angle : 0.701 17.109 28495 Z= 0.332 Chirality : 0.050 0.458 3398 Planarity : 0.004 0.075 3477 Dihedral : 11.435 101.457 4390 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.96 % Allowed : 14.74 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.17), residues: 2451 helix: 0.83 (0.29), residues: 391 sheet: -0.22 (0.20), residues: 719 loop : -2.24 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 273 TYR 0.017 0.001 TYR L 51 PHE 0.023 0.002 PHE E 522 TRP 0.019 0.001 TRP D 596 HIS 0.005 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00432 (20726) covalent geometry : angle 0.64721 (28164) SS BOND : bond 0.00433 ( 38) SS BOND : angle 1.36248 ( 76) hydrogen bonds : bond 0.04008 ( 622) hydrogen bonds : angle 5.02963 ( 1725) link_ALPHA1-2 : bond 0.00494 ( 4) link_ALPHA1-2 : angle 3.27043 ( 12) link_ALPHA1-3 : bond 0.00977 ( 9) link_ALPHA1-3 : angle 1.74171 ( 27) link_ALPHA1-6 : bond 0.00740 ( 9) link_ALPHA1-6 : angle 1.83731 ( 27) link_BETA1-4 : bond 0.00509 ( 21) link_BETA1-4 : angle 1.85694 ( 63) link_NAG-ASN : bond 0.00779 ( 42) link_NAG-ASN : angle 3.49288 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 112 TRP cc_start: 0.8114 (t-100) cc_final: 0.7688 (t-100) REVERT: B 342 LEU cc_start: 0.8286 (tp) cc_final: 0.7855 (tp) REVERT: C 154 MET cc_start: 0.8817 (mtp) cc_final: 0.8281 (mtp) REVERT: C 160 ASN cc_start: 0.7957 (t0) cc_final: 0.7187 (p0) REVERT: C 180 ASP cc_start: 0.8462 (t0) cc_final: 0.8239 (t70) REVERT: C 268 LYS cc_start: 0.8305 (mtmt) cc_final: 0.8105 (mtmt) REVERT: D 627 THR cc_start: 0.7880 (p) cc_final: 0.7602 (p) REVERT: F 585 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7870 (mtp85) REVERT: H 12 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7766 (mmmt) REVERT: L 37 TRP cc_start: 0.8458 (m100) cc_final: 0.8131 (m100) outliers start: 63 outliers final: 46 residues processed: 317 average time/residue: 0.1414 time to fit residues: 71.2446 Evaluate side-chains 320 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 592 LEU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 40 GLN Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 20 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 0.3980 chunk 111 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS B 478 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.158879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129446 restraints weight = 26717.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129560 restraints weight = 31268.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.130379 restraints weight = 29728.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.130686 restraints weight = 22829.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.130891 restraints weight = 21160.916| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1893 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= 0.134 Angle : 0.666 16.889 28495 Z= 0.313 Chirality : 0.048 0.451 3398 Planarity : 0.004 0.068 3477 Dihedral : 10.749 98.347 4390 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 2.86 % Allowed : 16.15 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2451 helix: 1.06 (0.29), residues: 389 sheet: -0.22 (0.20), residues: 728 loop : -2.18 (0.16), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 63 TYR 0.011 0.001 TYR J 51 PHE 0.022 0.001 PHE E 522 TRP 0.017 0.001 TRP D 596 HIS 0.007 0.001 HIS J 41 Details of bonding type rmsd covalent geometry : bond 0.00308 (20726) covalent geometry : angle 0.61417 (28164) SS BOND : bond 0.00302 ( 38) SS BOND : angle 1.31085 ( 76) hydrogen bonds : bond 0.03550 ( 622) hydrogen bonds : angle 4.86581 ( 1725) link_ALPHA1-2 : bond 0.00805 ( 4) link_ALPHA1-2 : angle 3.34455 ( 12) link_ALPHA1-3 : bond 0.01040 ( 9) link_ALPHA1-3 : angle 1.78225 ( 27) link_ALPHA1-6 : bond 0.00806 ( 9) link_ALPHA1-6 : angle 1.79056 ( 27) link_BETA1-4 : bond 0.00485 ( 21) link_BETA1-4 : angle 1.67263 ( 63) link_NAG-ASN : bond 0.00718 ( 42) link_NAG-ASN : angle 3.32511 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 283 time to evaluate : 0.797 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: 0.8057 (t-100) cc_final: 0.7717 (t-100) REVERT: B 342 LEU cc_start: 0.8202 (tp) cc_final: 0.7711 (tp) REVERT: C 154 MET cc_start: 0.8798 (mtp) cc_final: 0.8296 (mtp) REVERT: C 317 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.7736 (p90) REVERT: D 522 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4192 (t80) REVERT: D 627 THR cc_start: 0.7733 (p) cc_final: 0.7521 (p) REVERT: H 12 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7752 (mmmt) REVERT: L 37 TRP cc_start: 0.8433 (m100) cc_final: 0.8063 (m100) outliers start: 61 outliers final: 44 residues processed: 319 average time/residue: 0.1310 time to fit residues: 66.4236 Evaluate side-chains 319 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 273 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 230 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 150 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 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** L 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.158238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131665 restraints weight = 26559.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130684 restraints weight = 37451.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131651 restraints weight = 35452.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.131021 restraints weight = 28140.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131454 restraints weight = 26717.366| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20849 Z= 0.146 Angle : 0.669 16.667 28495 Z= 0.314 Chirality : 0.048 0.445 3398 Planarity : 0.004 0.077 3477 Dihedral : 10.227 96.733 4390 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.33 % Allowed : 16.53 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.17), residues: 2451 helix: 1.15 (0.29), residues: 390 sheet: -0.18 (0.20), residues: 713 loop : -2.13 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 617 TYR 0.010 0.001 TYR J 51 PHE 0.022 0.001 PHE E 522 TRP 0.017 0.001 TRP D 596 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00343 (20726) covalent geometry : angle 0.61913 (28164) SS BOND : bond 0.00301 ( 38) SS BOND : angle 1.20956 ( 76) hydrogen bonds : bond 0.03565 ( 622) hydrogen bonds : angle 4.73655 ( 1725) link_ALPHA1-2 : bond 0.00754 ( 4) link_ALPHA1-2 : angle 3.50942 ( 12) link_ALPHA1-3 : bond 0.00988 ( 9) link_ALPHA1-3 : angle 1.77864 ( 27) link_ALPHA1-6 : bond 0.00779 ( 9) link_ALPHA1-6 : angle 1.78543 ( 27) link_BETA1-4 : bond 0.00477 ( 21) link_BETA1-4 : angle 1.57889 ( 63) link_NAG-ASN : bond 0.00718 ( 42) link_NAG-ASN : angle 3.29778 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 277 time to evaluate : 0.790 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 259 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8380 (mp) REVERT: B 112 TRP cc_start: 0.8057 (t-100) cc_final: 0.7749 (t-100) REVERT: C 154 MET cc_start: 0.8855 (mtp) cc_final: 0.8352 (mtp) REVERT: C 317 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.7641 (p90) REVERT: D 522 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4265 (t80) REVERT: D 627 THR cc_start: 0.8012 (p) cc_final: 0.7630 (p) REVERT: F 585 ARG cc_start: 0.8091 (ttp80) cc_final: 0.7874 (mtp85) REVERT: H 12 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7763 (mmmt) REVERT: L 37 TRP cc_start: 0.8443 (m100) cc_final: 0.8037 (m100) outliers start: 71 outliers final: 54 residues processed: 322 average time/residue: 0.1327 time to fit residues: 67.0505 Evaluate side-chains 324 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain D residue 618 ASN Chi-restraints excluded: chain D residue 622 ILE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 210 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 16 optimal weight: 0.0670 chunk 205 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 195 ASN C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.155064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129738 restraints weight = 26678.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129175 restraints weight = 33739.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129616 restraints weight = 33988.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.129133 restraints weight = 27670.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129608 restraints weight = 27764.012| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20849 Z= 0.227 Angle : 0.746 16.736 28495 Z= 0.353 Chirality : 0.051 0.536 3398 Planarity : 0.004 0.081 3477 Dihedral : 10.270 99.477 4390 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.43 % Allowed : 17.23 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.17), residues: 2451 helix: 0.96 (0.29), residues: 392 sheet: -0.21 (0.20), residues: 718 loop : -2.25 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 166 TYR 0.014 0.002 TYR J 51 PHE 0.023 0.002 PHE E 522 TRP 0.017 0.002 TRP A 69 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00548 (20726) covalent geometry : angle 0.69402 (28164) SS BOND : bond 0.00404 ( 38) SS BOND : angle 1.56436 ( 76) hydrogen bonds : bond 0.04169 ( 622) hydrogen bonds : angle 4.83857 ( 1725) link_ALPHA1-2 : bond 0.00681 ( 4) link_ALPHA1-2 : angle 3.86502 ( 12) link_ALPHA1-3 : bond 0.00963 ( 9) link_ALPHA1-3 : angle 1.81300 ( 27) link_ALPHA1-6 : bond 0.00679 ( 9) link_ALPHA1-6 : angle 1.89991 ( 27) link_BETA1-4 : bond 0.00506 ( 21) link_BETA1-4 : angle 1.69064 ( 63) link_NAG-ASN : bond 0.00838 ( 42) link_NAG-ASN : angle 3.52474 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 280 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASN cc_start: 0.7620 (t0) cc_final: 0.7368 (t0) REVERT: A 259 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8566 (mp) REVERT: A 317 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7405 (p90) REVERT: B 112 TRP cc_start: 0.8094 (t-100) cc_final: 0.7661 (t-100) REVERT: B 342 LEU cc_start: 0.8442 (tp) cc_final: 0.8186 (tp) REVERT: C 154 MET cc_start: 0.8854 (mtp) cc_final: 0.8207 (mtp) REVERT: C 317 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.7812 (p90) REVERT: D 522 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.4695 (t80) REVERT: D 627 THR cc_start: 0.7927 (p) cc_final: 0.7657 (p) REVERT: F 585 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7901 (mtp85) REVERT: H 12 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7687 (mmmt) REVERT: L 37 TRP cc_start: 0.8482 (m100) cc_final: 0.8116 (m100) outliers start: 73 outliers final: 54 residues processed: 333 average time/residue: 0.1358 time to fit residues: 71.0786 Evaluate side-chains 329 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 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 595 ILE Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 29 PHE Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS C 302 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN G 119 GLN H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117082 restraints weight = 27346.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.115766 restraints weight = 34717.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116995 restraints weight = 37164.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.117224 restraints weight = 27616.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117450 restraints weight = 26513.322| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20849 Z= 0.138 Angle : 0.679 16.828 28495 Z= 0.318 Chirality : 0.048 0.470 3398 Planarity : 0.004 0.069 3477 Dihedral : 9.715 92.060 4390 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.86 % Allowed : 18.03 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.17), residues: 2451 helix: 1.19 (0.29), residues: 390 sheet: -0.14 (0.20), residues: 708 loop : -2.14 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 166 TYR 0.022 0.001 TYR G 116 PHE 0.022 0.001 PHE E 522 TRP 0.016 0.001 TRP D 596 HIS 0.019 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00319 (20726) covalent geometry : angle 0.62649 (28164) SS BOND : bond 0.00310 ( 38) SS BOND : angle 1.33654 ( 76) hydrogen bonds : bond 0.03497 ( 622) hydrogen bonds : angle 4.66972 ( 1725) link_ALPHA1-2 : bond 0.01022 ( 4) link_ALPHA1-2 : angle 3.62378 ( 12) link_ALPHA1-3 : bond 0.00980 ( 9) link_ALPHA1-3 : angle 1.78555 ( 27) link_ALPHA1-6 : bond 0.00782 ( 9) link_ALPHA1-6 : angle 1.76082 ( 27) link_BETA1-4 : bond 0.00474 ( 21) link_BETA1-4 : angle 1.55903 ( 63) link_NAG-ASN : bond 0.00715 ( 42) link_NAG-ASN : angle 3.40155 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 291 time to evaluate : 0.763 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 66 HIS cc_start: 0.6700 (m90) cc_final: 0.6479 (m-70) REVERT: A 259 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 417 GLN cc_start: 0.7812 (mt0) cc_final: 0.7509 (mt0) REVERT: B 112 TRP cc_start: 0.8015 (t-100) cc_final: 0.7705 (t-100) REVERT: B 342 LEU cc_start: 0.8288 (tp) cc_final: 0.8032 (tp) REVERT: B 449 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7940 (mt) REVERT: C 111 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8370 (tt) REVERT: C 154 MET cc_start: 0.8831 (mtp) cc_final: 0.8336 (mtp) REVERT: C 317 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.7739 (p90) REVERT: D 522 PHE cc_start: 0.6062 (OUTLIER) cc_final: 0.4581 (t80) REVERT: D 627 THR cc_start: 0.7888 (p) cc_final: 0.7676 (p) REVERT: F 585 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7849 (mtp85) REVERT: H 12 LYS cc_start: 0.8006 (mmtp) cc_final: 0.7748 (mmmt) REVERT: L 37 TRP cc_start: 0.8426 (m100) cc_final: 0.8001 (m100) outliers start: 61 outliers final: 47 residues processed: 332 average time/residue: 0.1381 time to fit residues: 73.0284 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 : 0.965 ------------------------------------------------------------------------------- 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 259 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 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 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 45 TRP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 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 595 ILE Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 75 SER Chi-restraints excluded: chain G residue 119 GLN Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 30 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 91 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 8 optimal weight: 0.0060 chunk 229 optimal weight: 0.7980 chunk 206 optimal weight: 0.1980 chunk 159 optimal weight: 0.8980 chunk 101 optimal weight: 0.0020 chunk 31 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 213 optimal weight: 0.2980 chunk 126 optimal weight: 0.5980 overall best weight: 0.2204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 425 ASN ** 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** L 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.160543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134299 restraints weight = 26746.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133488 restraints weight = 39867.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134617 restraints weight = 35951.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134232 restraints weight = 29561.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134847 restraints weight = 26866.291| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 20849 Z= 0.109 Angle : 0.640 15.397 28495 Z= 0.301 Chirality : 0.047 0.425 3398 Planarity : 0.004 0.060 3477 Dihedral : 9.005 80.691 4390 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.16 % Allowed : 19.15 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2451 helix: 1.25 (0.29), residues: 400 sheet: -0.07 (0.20), residues: 735 loop : -1.98 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 166 TYR 0.012 0.001 TYR C 486 PHE 0.021 0.001 PHE E 522 TRP 0.017 0.001 TRP G 117 HIS 0.004 0.001 HIS C 249 Details of bonding type rmsd covalent geometry : bond 0.00232 (20726) covalent geometry : angle 0.59285 (28164) SS BOND : bond 0.00276 ( 38) SS BOND : angle 1.08195 ( 76) hydrogen bonds : bond 0.02954 ( 622) hydrogen bonds : angle 4.48929 ( 1725) link_ALPHA1-2 : bond 0.01129 ( 4) link_ALPHA1-2 : angle 3.33244 ( 12) link_ALPHA1-3 : bond 0.00999 ( 9) link_ALPHA1-3 : angle 1.79475 ( 27) link_ALPHA1-6 : bond 0.00938 ( 9) link_ALPHA1-6 : angle 1.64988 ( 27) link_BETA1-4 : bond 0.00481 ( 21) link_BETA1-4 : angle 1.40764 ( 63) link_NAG-ASN : bond 0.00677 ( 42) link_NAG-ASN : angle 3.17762 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 0.637 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 201 CYS cc_start: 0.8151 (m) cc_final: 0.7811 (m) REVERT: A 317 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.7724 (p90) REVERT: A 417 GLN cc_start: 0.7878 (mt0) cc_final: 0.7595 (mt0) REVERT: B 112 TRP cc_start: 0.8014 (t-100) cc_final: 0.7665 (t-100) REVERT: B 342 LEU cc_start: 0.8193 (tp) cc_final: 0.7945 (tp) REVERT: C 154 MET cc_start: 0.8857 (mtp) cc_final: 0.8368 (mtp) REVERT: C 180 ASP cc_start: 0.8389 (t0) cc_final: 0.8131 (t70) REVERT: C 424 ILE cc_start: 0.8979 (mm) cc_final: 0.8608 (mm) REVERT: D 522 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.4552 (t80) REVERT: D 627 THR cc_start: 0.7863 (p) cc_final: 0.7494 (p) REVERT: G 89 ASP cc_start: 0.7993 (t70) cc_final: 0.7729 (t0) REVERT: H 12 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7690 (mmmt) REVERT: I 54 ASN cc_start: 0.8501 (m-40) cc_final: 0.8049 (m-40) REVERT: L 37 TRP cc_start: 0.8426 (m100) cc_final: 0.7991 (m100) outliers start: 46 outliers final: 31 residues processed: 331 average time/residue: 0.1367 time to fit residues: 71.7279 Evaluate side-chains 320 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 161 THR 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 323 ILE Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 74 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 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 213 optimal weight: 0.0470 chunk 139 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 39 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- 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** ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN L 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.131695 restraints weight = 26971.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.130656 restraints weight = 38091.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132134 restraints weight = 35461.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.131476 restraints weight = 27994.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131981 restraints weight = 28086.810| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20849 Z= 0.151 Angle : 0.687 17.371 28495 Z= 0.325 Chirality : 0.048 0.579 3398 Planarity : 0.004 0.070 3477 Dihedral : 8.778 67.979 4390 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 1.83 % Allowed : 19.30 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.17), residues: 2451 helix: 1.14 (0.29), residues: 401 sheet: -0.10 (0.19), residues: 741 loop : -2.00 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 166 TYR 0.018 0.001 TYR B 217 PHE 0.021 0.001 PHE E 522 TRP 0.044 0.001 TRP D 631 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (20726) covalent geometry : angle 0.63568 (28164) SS BOND : bond 0.00573 ( 38) SS BOND : angle 1.74848 ( 76) hydrogen bonds : bond 0.03348 ( 622) hydrogen bonds : angle 4.48468 ( 1725) link_ALPHA1-2 : bond 0.00800 ( 4) link_ALPHA1-2 : angle 3.49466 ( 12) link_ALPHA1-3 : bond 0.00907 ( 9) link_ALPHA1-3 : angle 1.80289 ( 27) link_ALPHA1-6 : bond 0.00778 ( 9) link_ALPHA1-6 : angle 1.66952 ( 27) link_BETA1-4 : bond 0.00476 ( 21) link_BETA1-4 : angle 1.43149 ( 63) link_NAG-ASN : bond 0.00758 ( 42) link_NAG-ASN : angle 3.33587 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4902 Ramachandran restraints generated. 2451 Oldfield, 0 Emsley, 2451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 288 time to evaluate : 0.780 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: 0.8487 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 417 GLN cc_start: 0.7843 (mt0) cc_final: 0.7560 (mt0) REVERT: B 112 TRP cc_start: 0.8008 (t-100) cc_final: 0.7685 (t-100) REVERT: B 342 LEU cc_start: 0.8304 (tp) cc_final: 0.8063 (tp) REVERT: C 154 MET cc_start: 0.8870 (mtp) cc_final: 0.8380 (mtp) REVERT: C 180 ASP cc_start: 0.8517 (t0) cc_final: 0.8223 (t70) REVERT: C 424 ILE cc_start: 0.8973 (mm) cc_final: 0.8628 (mm) REVERT: D 522 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4809 (t80) REVERT: D 621 GLU cc_start: 0.8026 (pp20) cc_final: 0.7129 (pp20) REVERT: D 627 THR cc_start: 0.7916 (p) cc_final: 0.7580 (p) REVERT: G 89 ASP cc_start: 0.7944 (t70) cc_final: 0.7729 (t0) REVERT: I 54 ASN cc_start: 0.8485 (m-40) cc_final: 0.8016 (m-40) REVERT: L 37 TRP cc_start: 0.8452 (m100) cc_final: 0.8051 (m100) outliers start: 39 outliers final: 35 residues processed: 317 average time/residue: 0.1400 time to fit residues: 70.2444 Evaluate side-chains 316 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 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 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 363 GLN Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 630 GLN Chi-restraints excluded: chain E residue 518 VAL Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain F residue 604 CYS Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H 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 91 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 147 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 186 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.113916 restraints weight = 27572.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.112614 restraints weight = 34640.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.113767 restraints weight = 35099.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113994 restraints weight = 27377.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.114181 restraints weight = 27707.734| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 20849 Z= 0.239 Angle : 0.791 17.132 28495 Z= 0.377 Chirality : 0.051 0.564 3398 Planarity : 0.004 0.084 3477 Dihedral : 9.125 73.545 4390 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 2.44 % Allowed : 19.20 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.17), residues: 2451 helix: 0.83 (0.28), residues: 404 sheet: -0.17 (0.20), residues: 730 loop : -2.17 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 166 TYR 0.017 0.002 TYR B 217 PHE 0.024 0.002 PHE E 522 TRP 0.029 0.002 TRP E 631 HIS 0.006 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00577 (20726) covalent geometry : angle 0.73716 (28164) SS BOND : bond 0.00545 ( 38) SS BOND : angle 2.02720 ( 76) hydrogen bonds : bond 0.04393 ( 622) hydrogen bonds : angle 4.79172 ( 1725) link_ALPHA1-2 : bond 0.00561 ( 4) link_ALPHA1-2 : angle 3.35956 ( 12) link_ALPHA1-3 : bond 0.00891 ( 9) link_ALPHA1-3 : angle 1.90183 ( 27) link_ALPHA1-6 : bond 0.00696 ( 9) link_ALPHA1-6 : angle 1.84814 ( 27) link_BETA1-4 : bond 0.00558 ( 21) link_BETA1-4 : angle 1.69042 ( 63) link_NAG-ASN : bond 0.00859 ( 42) link_NAG-ASN : angle 3.70426 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3113.94 seconds wall clock time: 54 minutes 54.59 seconds (3294.59 seconds total)