Starting phenix.real_space_refine on Mon Apr 6 12:28:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.map" model { file = "/net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x97_22103/04_2026/6x97_22103.cif" } resolution = 3.65 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= 0.070 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 129 5.16 5 C 11862 2.51 5 N 3171 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18873 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "B" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "H" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "D" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "G" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3373 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 22, 'TRANS': 404} Chain breaks: 4 Chain: "I" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 938 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "J" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 899 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "K" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 804 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} 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: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} 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: "G" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} 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 Time building chain proxies: 4.10, per 1000 atoms: 0.22 Number of scatterers: 18873 At special positions: 0 Unit cell: (145.41, 158.51, 115.28, 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 129 16.00 O 3711 8.00 N 3171 7.00 C 11862 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.12 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=2.04 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=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.06 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.07 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 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=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.06 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.07 Simple disulfide: pdb=" SG CYS E 35A" - pdb=" SG CYS E 50 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.12 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.06 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.10 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.07 Simple disulfide: pdb=" SG CYS J 35A" - pdb=" SG CYS J 50 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 608 " - " ASN A 332 " " NAG A 611 " - " ASN A 234 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 156 " " NAG A 614 " - " ASN A 160 " " NAG A 615 " - " ASN A 392 " " NAG A 616 " - " ASN A 197 " " NAG A 619 " - " ASN A 339 " " NAG A 620 " - " ASN A 133 " " NAG C 608 " - " ASN C 332 " " NAG C 611 " - " ASN C 234 " " NAG C 612 " - " ASN C 386 " " NAG C 613 " - " ASN C 156 " " NAG C 614 " - " ASN C 160 " " NAG C 615 " - " ASN C 392 " " NAG C 616 " - " ASN C 197 " " NAG C 619 " - " ASN C 339 " " NAG C 620 " - " ASN C 133 " " NAG G 608 " - " ASN G 332 " " NAG G 611 " - " ASN G 234 " " NAG G 612 " - " ASN G 386 " " NAG G 613 " - " ASN G 156 " " NAG G 614 " - " ASN G 160 " " NAG G 615 " - " ASN G 392 " " NAG G 616 " - " ASN G 197 " " NAG G 619 " - " ASN G 339 " " NAG G 620 " - " ASN G 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 88 " " NAG Q 1 " - " ASN A 363 " " NAG R 1 " - " ASN C 448 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 295 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 363 " " NAG W 1 " - " ASN G 448 " " NAG X 1 " - " ASN G 262 " " NAG Y 1 " - " ASN G 295 " " NAG Z 1 " - " ASN G 88 " " NAG a 1 " - " ASN G 363 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 701.2 milliseconds 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4260 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 48 sheets defined 19.3% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 351 removed outlier: 4.008A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 351 removed outlier: 4.008A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 480 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.655A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'G' and resid 98 through 117 removed outlier: 4.079A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 139 through 151 Processing helix chain 'G' and resid 335 through 351 removed outlier: 4.007A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 480 Processing helix chain 'G' and resid 481 through 483 No H-bonds generated for 'chain 'G' and resid 481 through 483' Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 541 removed outlier: 3.654A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 596 removed outlier: 4.016A pdb=" N LYS I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLN I 575 " --> pdb=" O TRP I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 615 Processing helix chain 'I' and resid 618 through 626 removed outlier: 4.613A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 652 removed outlier: 3.542A pdb=" N GLN I 650 " --> pdb=" O LEU I 646 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.887A 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 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.617A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.078A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 56 " --> pdb=" O PHE H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER H 96 " --> pdb=" O GLY H 100E" (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLY H 100E" --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR H 98 " --> pdb=" O GLY H 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY H 100C" --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.541A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.886A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER C 375 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 261 Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.517A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 56 " --> pdb=" O PHE E 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.604A pdb=" N LEU E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER E 96 " --> pdb=" O GLY E 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY E 100E" --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR E 98 " --> pdb=" O GLY E 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY E 100C" --> pdb=" O THR E 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL F 11 " --> pdb=" O VAL F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 499 removed outlier: 5.314A pdb=" N VAL I 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL G 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR I 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N TYR G 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N CYS I 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.887A pdb=" N CYS G 54 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.072A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 256 through 257 removed outlier: 3.618A pdb=" N SER G 375 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR G 450 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N CYS G 296 " --> pdb=" O VAL G 442 " (cutoff:3.500A) removed outlier: 10.375A pdb=" N VAL G 442 " --> pdb=" O CYS G 296 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 261 Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 6.921A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.518A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 11 removed outlier: 3.603A pdb=" N LEU J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER J 96 " --> pdb=" O GLY J 100E" (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY J 100E" --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR J 98 " --> pdb=" O GLY J 100C" (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY J 100C" --> pdb=" O THR J 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'K' and resid 11 through 12 removed outlier: 6.553A pdb=" N VAL K 11 " --> pdb=" O VAL K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.540A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 690 hydrogen bonds defined for protein. 1800 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: 3.43 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3809 1.32 - 1.46: 6249 1.46 - 1.59: 8957 1.59 - 1.73: 80 1.73 - 1.87: 162 Bond restraints: 19257 Sorted by residual: bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CB ILE F 2 " pdb=" CG1 ILE F 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" CB ILE K 2 " pdb=" CG1 ILE K 2 " ideal model delta sigma weight residual 1.530 1.669 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CB HIS C 85 " pdb=" CG HIS C 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 bond pdb=" CB HIS A 85 " pdb=" CG HIS A 85 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.06e+01 ... (remaining 19252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 24178 3.18 - 6.37: 1834 6.37 - 9.55: 133 9.55 - 12.73: 9 12.73 - 15.92: 3 Bond angle restraints: 26157 Sorted by residual: angle pdb=" N VAL L 3 " pdb=" CA VAL L 3 " pdb=" C VAL L 3 " ideal model delta sigma weight residual 111.62 118.48 -6.86 7.90e-01 1.60e+00 7.55e+01 angle pdb=" N VAL F 3 " pdb=" CA VAL F 3 " pdb=" C VAL F 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" N VAL K 3 " pdb=" CA VAL K 3 " pdb=" C VAL K 3 " ideal model delta sigma weight residual 111.62 118.47 -6.85 7.90e-01 1.60e+00 7.52e+01 angle pdb=" C ARG G 298 " pdb=" N PRO G 299 " pdb=" CA PRO G 299 " ideal model delta sigma weight residual 119.56 127.63 -8.07 1.01e+00 9.80e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.62 -8.06 1.01e+00 9.80e-01 6.37e+01 ... (remaining 26152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.18: 11865 21.18 - 42.36: 234 42.36 - 63.54: 90 63.54 - 84.72: 51 84.72 - 105.90: 15 Dihedral angle restraints: 12255 sinusoidal: 5622 harmonic: 6633 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.70 -80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual 93.00 173.69 -80.69 1 1.00e+01 1.00e-02 8.05e+01 ... (remaining 12252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2091 0.105 - 0.210: 694 0.210 - 0.315: 187 0.315 - 0.420: 107 0.420 - 0.525: 47 Chirality restraints: 3126 Sorted by residual: chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.17e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.16e+02 chirality pdb=" C1 BMA X 3 " pdb=" O4 NAG X 2 " pdb=" C2 BMA X 3 " pdb=" O5 BMA X 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.14e+02 ... (remaining 3123 not shown) Planarity restraints: 3285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.086 2.00e-02 2.50e+03 8.83e-02 9.76e+01 pdb=" CG ASN A 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG A 619 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 339 " -0.086 2.00e-02 2.50e+03 8.83e-02 9.75e+01 pdb=" CG ASN C 339 " 0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN C 339 " 0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 339 " 0.135 2.00e-02 2.50e+03 pdb=" C1 NAG C 619 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 339 " 0.085 2.00e-02 2.50e+03 8.81e-02 9.70e+01 pdb=" CG ASN G 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN G 339 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN G 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG G 619 " 0.107 2.00e-02 2.50e+03 ... (remaining 3282 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 9760 2.98 - 3.46: 16783 3.46 - 3.94: 31799 3.94 - 4.42: 36193 4.42 - 4.90: 56800 Nonbonded interactions: 151335 Sorted by model distance: nonbonded pdb=" N THR C 50 " pdb=" O THR C 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR A 50 " pdb=" O THR A 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR G 50 " pdb=" O THR G 50 " model vdw 2.496 2.496 nonbonded pdb=" N THR C 303 " pdb=" O THR C 303 " model vdw 2.508 2.496 nonbonded pdb=" N THR A 303 " pdb=" O THR A 303 " model vdw 2.508 2.496 ... (remaining 151330 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'S' 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: 1.720 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.180 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 : 0.022 0.139 19359 Z= 1.168 Angle : 1.792 15.917 26421 Z= 1.162 Chirality : 0.138 0.525 3126 Planarity : 0.009 0.044 3243 Dihedral : 11.601 105.896 7869 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.17), residues: 2265 helix: -0.76 (0.25), residues: 342 sheet: 0.52 (0.19), residues: 672 loop : 0.54 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 166 TYR 0.078 0.010 TYR I 638 PHE 0.031 0.007 PHE C 383 TRP 0.064 0.011 TRP I 628 HIS 0.010 0.003 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.02184 (19257) covalent geometry : angle 1.76796 (26157) SS BOND : bond 0.03461 ( 42) SS BOND : angle 2.86792 ( 84) hydrogen bonds : bond 0.18936 ( 672) hydrogen bonds : angle 8.00896 ( 1800) link_BETA1-4 : bond 0.07608 ( 18) link_BETA1-4 : angle 4.76795 ( 54) link_NAG-ASN : bond 0.08233 ( 42) link_NAG-ASN : angle 2.99682 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 534 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: A 427 TRP cc_start: 0.7051 (m-10) cc_final: 0.6625 (m-10) REVERT: B 586 TYR cc_start: 0.8766 (t80) cc_final: 0.8543 (t80) REVERT: B 627 THR cc_start: 0.8108 (m) cc_final: 0.7760 (p) REVERT: B 628 TRP cc_start: 0.8452 (t-100) cc_final: 0.8011 (t-100) REVERT: B 657 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7789 (mt-10) REVERT: H 45 LEU cc_start: 0.7735 (mt) cc_final: 0.7391 (mt) REVERT: C 133 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: D 607 ASN cc_start: 0.8216 (m-40) cc_final: 0.7964 (m110) REVERT: D 627 THR cc_start: 0.7876 (m) cc_final: 0.7384 (p) REVERT: D 628 TRP cc_start: 0.8389 (t-100) cc_final: 0.8145 (t-100) REVERT: D 657 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7489 (mt-10) REVERT: E 45 LEU cc_start: 0.7359 (mt) cc_final: 0.6857 (mt) REVERT: E 84 VAL cc_start: 0.8679 (m) cc_final: 0.8460 (t) REVERT: G 150 MET cc_start: 0.7754 (mmm) cc_final: 0.7322 (mmm) REVERT: G 173 TYR cc_start: 0.8079 (p90) cc_final: 0.7798 (p90) REVERT: G 271 MET cc_start: 0.7796 (mmm) cc_final: 0.7570 (mmm) REVERT: G 427 TRP cc_start: 0.7025 (m-10) cc_final: 0.6654 (m-10) outliers start: 6 outliers final: 1 residues processed: 540 average time/residue: 0.1509 time to fit residues: 121.0813 Evaluate side-chains 298 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 295 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** A 249 HIS ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN B 577 GLN B 591 GLN L 6 GLN C 195 ASN C 249 HIS C 258 GLN C 425 ASN D 630 GLN F 6 GLN G 130 GLN G 195 ASN G 249 HIS G 425 ASN ** I 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 607 ASN K 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.142489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.121358 restraints weight = 31428.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.124352 restraints weight = 19349.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.126315 restraints weight = 13865.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127778 restraints weight = 10945.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128695 restraints weight = 9180.432| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19359 Z= 0.189 Angle : 0.773 8.781 26421 Z= 0.402 Chirality : 0.049 0.198 3126 Planarity : 0.004 0.037 3243 Dihedral : 8.219 70.857 3729 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.40 % Allowed : 8.36 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.17), residues: 2265 helix: 0.55 (0.28), residues: 348 sheet: 0.28 (0.18), residues: 777 loop : 0.03 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 43 TYR 0.021 0.002 TYR D 643 PHE 0.025 0.002 PHE J 52 TRP 0.015 0.002 TRP G 479 HIS 0.005 0.001 HIS G 72 Details of bonding type rmsd covalent geometry : bond 0.00410 (19257) covalent geometry : angle 0.73273 (26157) SS BOND : bond 0.00250 ( 42) SS BOND : angle 1.03865 ( 84) hydrogen bonds : bond 0.06457 ( 672) hydrogen bonds : angle 6.37892 ( 1800) link_BETA1-4 : bond 0.00678 ( 18) link_BETA1-4 : angle 3.02034 ( 54) link_NAG-ASN : bond 0.00489 ( 42) link_NAG-ASN : angle 3.03725 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 385 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8174 (m-80) cc_final: 0.7971 (m-10) REVERT: C 318 TYR cc_start: 0.7788 (m-80) cc_final: 0.7534 (m-80) REVERT: D 588 ARG cc_start: 0.8288 (tpt-90) cc_final: 0.8063 (tpp80) REVERT: D 617 ARG cc_start: 0.7186 (mtp-110) cc_final: 0.6716 (mtp-110) REVERT: D 630 GLN cc_start: 0.8400 (mt0) cc_final: 0.8062 (mt0) REVERT: D 648 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8300 (pt0) REVERT: D 651 ASN cc_start: 0.6439 (p0) cc_final: 0.6198 (p0) REVERT: E 45 LEU cc_start: 0.7537 (mt) cc_final: 0.7043 (mt) REVERT: G 150 MET cc_start: 0.7434 (mmm) cc_final: 0.7226 (mmm) REVERT: G 161 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6164 (ttm) REVERT: G 173 TYR cc_start: 0.7932 (p90) cc_final: 0.7651 (p90) REVERT: G 318 TYR cc_start: 0.7969 (m-80) cc_final: 0.7661 (m-80) REVERT: I 607 ASN cc_start: 0.8275 (m-40) cc_final: 0.8008 (m110) REVERT: I 610 TRP cc_start: 0.8182 (t-100) cc_final: 0.7793 (t-100) REVERT: I 617 ARG cc_start: 0.7514 (mtp-110) cc_final: 0.7060 (mtp-110) REVERT: I 625 ASN cc_start: 0.8811 (m-40) cc_final: 0.8148 (t0) REVERT: I 648 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8601 (mm-30) REVERT: I 650 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: K 24 GLN cc_start: 0.7374 (mt0) cc_final: 0.7164 (tt0) outliers start: 48 outliers final: 27 residues processed: 411 average time/residue: 0.1452 time to fit residues: 90.2657 Evaluate side-chains 338 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 309 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 184 ILE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 212 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN L 24 GLN L 27 GLN C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 607 ASN F 27 GLN G 103 GLN G 195 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.121103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100632 restraints weight = 32803.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103035 restraints weight = 21624.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104675 restraints weight = 16159.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.105739 restraints weight = 13128.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106622 restraints weight = 11339.525| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19359 Z= 0.171 Angle : 0.676 8.898 26421 Z= 0.351 Chirality : 0.046 0.170 3126 Planarity : 0.004 0.040 3243 Dihedral : 6.621 45.920 3727 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.10 % Allowed : 9.76 % Favored : 87.14 % 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 are not related in a simple way. whole: 0.08 (0.18), residues: 2265 helix: 0.34 (0.28), residues: 363 sheet: 0.27 (0.18), residues: 795 loop : -0.08 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 298 TYR 0.020 0.002 TYR H 90 PHE 0.017 0.002 PHE C 376 TRP 0.022 0.002 TRP D 628 HIS 0.004 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00388 (19257) covalent geometry : angle 0.64819 (26157) SS BOND : bond 0.00225 ( 42) SS BOND : angle 0.92895 ( 84) hydrogen bonds : bond 0.05080 ( 672) hydrogen bonds : angle 5.91980 ( 1800) link_BETA1-4 : bond 0.00744 ( 18) link_BETA1-4 : angle 2.30085 ( 54) link_NAG-ASN : bond 0.00399 ( 42) link_NAG-ASN : angle 2.42575 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 355 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 536 THR cc_start: 0.7474 (p) cc_final: 0.7193 (p) REVERT: B 545 LEU cc_start: 0.8303 (mt) cc_final: 0.8024 (mt) REVERT: B 648 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8183 (pt0) REVERT: B 649 SER cc_start: 0.9366 (m) cc_final: 0.8916 (t) REVERT: B 650 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: C 39 TYR cc_start: 0.8318 (m-80) cc_final: 0.7873 (m-10) REVERT: D 586 TYR cc_start: 0.8264 (t80) cc_final: 0.8051 (t80) REVERT: D 593 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7290 (mp) REVERT: D 595 ILE cc_start: 0.9183 (tp) cc_final: 0.8954 (tt) REVERT: D 617 ARG cc_start: 0.7124 (mtp-110) cc_final: 0.6699 (mtp-110) REVERT: D 648 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8259 (pt0) REVERT: D 650 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: F 91 THR cc_start: 0.8591 (p) cc_final: 0.8185 (p) REVERT: G 161 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6282 (ttt) REVERT: I 542 ARG cc_start: 0.8322 (ttm170) cc_final: 0.7556 (ttm170) REVERT: I 610 TRP cc_start: 0.8199 (t-100) cc_final: 0.7669 (t-100) REVERT: I 617 ARG cc_start: 0.7584 (mtp-110) cc_final: 0.7304 (mtp-110) REVERT: I 648 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8147 (pt0) REVERT: I 649 SER cc_start: 0.9184 (m) cc_final: 0.8950 (t) REVERT: I 650 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: I 651 ASN cc_start: 0.6241 (p0) cc_final: 0.5797 (p0) REVERT: K 69 THR cc_start: 0.8634 (p) cc_final: 0.8237 (p) REVERT: K 77 ASP cc_start: 0.7668 (m-30) cc_final: 0.7099 (m-30) outliers start: 62 outliers final: 34 residues processed: 383 average time/residue: 0.1440 time to fit residues: 84.2143 Evaluate side-chains 343 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 538 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 194 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 217 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 160 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN L 32 HIS L 70 GLN C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS G 103 GLN G 195 ASN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 591 GLN K 32 HIS K 70 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.093855 restraints weight = 33366.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096333 restraints weight = 21666.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098087 restraints weight = 15995.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.099320 restraints weight = 12948.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100111 restraints weight = 11099.393| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19359 Z= 0.229 Angle : 0.719 8.756 26421 Z= 0.369 Chirality : 0.047 0.180 3126 Planarity : 0.004 0.046 3243 Dihedral : 6.028 42.549 3727 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.20 % Allowed : 12.16 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 2265 helix: 0.27 (0.28), residues: 369 sheet: 0.15 (0.18), residues: 822 loop : -0.20 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 56 TYR 0.029 0.002 TYR I 586 PHE 0.025 0.002 PHE C 376 TRP 0.023 0.002 TRP B 628 HIS 0.005 0.002 HIS G 330 Details of bonding type rmsd covalent geometry : bond 0.00533 (19257) covalent geometry : angle 0.69291 (26157) SS BOND : bond 0.00568 ( 42) SS BOND : angle 1.03442 ( 84) hydrogen bonds : bond 0.05040 ( 672) hydrogen bonds : angle 5.89454 ( 1800) link_BETA1-4 : bond 0.00522 ( 18) link_BETA1-4 : angle 2.08621 ( 54) link_NAG-ASN : bond 0.00465 ( 42) link_NAG-ASN : angle 2.45096 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 326 time to evaluate : 0.731 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: B 545 LEU cc_start: 0.8434 (mt) cc_final: 0.8139 (mt) REVERT: B 634 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8231 (mm-30) REVERT: B 648 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8081 (pt0) REVERT: B 649 SER cc_start: 0.9262 (m) cc_final: 0.8874 (t) REVERT: B 650 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: C 39 TYR cc_start: 0.8541 (m-80) cc_final: 0.7974 (m-10) REVERT: D 535 MET cc_start: 0.7597 (mmm) cc_final: 0.6813 (mmm) REVERT: D 542 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.8125 (tpp80) REVERT: D 593 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7578 (mp) REVERT: D 617 ARG cc_start: 0.7212 (mtp-110) cc_final: 0.6886 (mtp-110) REVERT: D 648 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8198 (pt0) REVERT: D 650 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: D 651 ASN cc_start: 0.6527 (p0) cc_final: 0.6225 (p0) REVERT: G 42 VAL cc_start: 0.9124 (m) cc_final: 0.8914 (p) REVERT: I 648 GLU cc_start: 0.8737 (mm-30) cc_final: 0.7956 (pt0) REVERT: I 650 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: I 651 ASN cc_start: 0.6261 (p0) cc_final: 0.5991 (p0) REVERT: K 69 THR cc_start: 0.8752 (p) cc_final: 0.8368 (p) outliers start: 64 outliers final: 45 residues processed: 362 average time/residue: 0.1543 time to fit residues: 83.1898 Evaluate side-chains 326 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 545 LEU Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 164 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 224 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 208 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.094980 restraints weight = 33345.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.097582 restraints weight = 21490.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099231 restraints weight = 15829.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100569 restraints weight = 12851.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101347 restraints weight = 10970.402| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19359 Z= 0.156 Angle : 0.638 7.787 26421 Z= 0.325 Chirality : 0.045 0.168 3126 Planarity : 0.004 0.038 3243 Dihedral : 5.544 39.772 3723 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.85 % Allowed : 14.46 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.18), residues: 2265 helix: 0.44 (0.29), residues: 369 sheet: 0.19 (0.18), residues: 819 loop : -0.26 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 56 TYR 0.015 0.002 TYR D 586 PHE 0.014 0.001 PHE G 383 TRP 0.015 0.001 TRP B 628 HIS 0.003 0.001 HIS G 105 Details of bonding type rmsd covalent geometry : bond 0.00357 (19257) covalent geometry : angle 0.61485 (26157) SS BOND : bond 0.00251 ( 42) SS BOND : angle 0.85312 ( 84) hydrogen bonds : bond 0.04460 ( 672) hydrogen bonds : angle 5.64119 ( 1800) link_BETA1-4 : bond 0.00601 ( 18) link_BETA1-4 : angle 1.72969 ( 54) link_NAG-ASN : bond 0.00294 ( 42) link_NAG-ASN : angle 2.24543 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 291 time to evaluate : 0.673 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 102 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6988 (tm-30) REVERT: B 535 MET cc_start: 0.7788 (mmm) cc_final: 0.6612 (mmp) REVERT: B 545 LEU cc_start: 0.8579 (mt) cc_final: 0.8301 (mt) REVERT: B 634 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8294 (mm-30) REVERT: B 648 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7940 (pt0) REVERT: B 649 SER cc_start: 0.9302 (m) cc_final: 0.8925 (t) REVERT: B 650 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 656 ASN cc_start: 0.7305 (t0) cc_final: 0.6851 (t0) REVERT: H 6 GLU cc_start: 0.6634 (mp0) cc_final: 0.6426 (mp0) REVERT: C 39 TYR cc_start: 0.8472 (m-80) cc_final: 0.7843 (m-10) REVERT: C 427 TRP cc_start: 0.8312 (m100) cc_final: 0.7919 (m100) REVERT: D 542 ARG cc_start: 0.8577 (ttp-170) cc_final: 0.8234 (tpp80) REVERT: D 593 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7555 (mp) REVERT: D 617 ARG cc_start: 0.7150 (mtp-110) cc_final: 0.6938 (mtp-110) REVERT: D 648 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8324 (pt0) REVERT: D 650 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: D 656 ASN cc_start: 0.7534 (t0) cc_final: 0.6715 (t0) REVERT: F 91 THR cc_start: 0.8743 (p) cc_final: 0.8351 (p) REVERT: G 427 TRP cc_start: 0.7357 (m-10) cc_final: 0.6366 (m-90) REVERT: I 607 ASN cc_start: 0.8213 (m-40) cc_final: 0.7810 (m-40) REVERT: I 650 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: I 656 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.6685 (m110) REVERT: J 23 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7903 (pttm) REVERT: J 81 MET cc_start: 0.7576 (mtt) cc_final: 0.7369 (mtt) REVERT: J 110 THR cc_start: 0.7362 (m) cc_final: 0.7150 (m) outliers start: 57 outliers final: 43 residues processed: 325 average time/residue: 0.1416 time to fit residues: 69.9397 Evaluate side-chains 309 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 650 GLN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 3 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 140 optimal weight: 0.0020 chunk 137 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 198 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 192 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096736 restraints weight = 32888.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.099343 restraints weight = 20968.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.101083 restraints weight = 15335.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.102381 restraints weight = 12320.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103187 restraints weight = 10476.061| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19359 Z= 0.123 Angle : 0.605 8.066 26421 Z= 0.307 Chirality : 0.044 0.161 3126 Planarity : 0.004 0.033 3243 Dihedral : 5.228 38.078 3723 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.80 % Allowed : 14.96 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.18), residues: 2265 helix: 0.68 (0.30), residues: 345 sheet: 0.23 (0.18), residues: 816 loop : -0.23 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 28 TYR 0.015 0.001 TYR F 49 PHE 0.018 0.001 PHE F 98 TRP 0.027 0.001 TRP B 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00273 (19257) covalent geometry : angle 0.58466 (26157) SS BOND : bond 0.00216 ( 42) SS BOND : angle 0.76130 ( 84) hydrogen bonds : bond 0.04141 ( 672) hydrogen bonds : angle 5.50899 ( 1800) link_BETA1-4 : bond 0.00600 ( 18) link_BETA1-4 : angle 1.56549 ( 54) link_NAG-ASN : bond 0.00279 ( 42) link_NAG-ASN : angle 2.06932 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.512 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 102 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6825 (tm-30) REVERT: B 535 MET cc_start: 0.7730 (mmm) cc_final: 0.6650 (mmp) REVERT: B 545 LEU cc_start: 0.8627 (mt) cc_final: 0.8286 (mt) REVERT: B 648 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7827 (pt0) REVERT: B 649 SER cc_start: 0.9358 (m) cc_final: 0.8981 (t) REVERT: B 650 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: C 39 TYR cc_start: 0.8438 (m-80) cc_final: 0.7808 (m-10) REVERT: C 150 MET cc_start: 0.7182 (mmm) cc_final: 0.6872 (mmt) REVERT: C 427 TRP cc_start: 0.8357 (m100) cc_final: 0.7993 (m100) REVERT: D 530 MET cc_start: 0.8080 (mmm) cc_final: 0.7619 (mmm) REVERT: D 542 ARG cc_start: 0.8502 (ttp-170) cc_final: 0.8091 (ttm170) REVERT: D 610 TRP cc_start: 0.8087 (t-100) cc_final: 0.7679 (t-100) REVERT: D 648 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8065 (pt0) REVERT: D 656 ASN cc_start: 0.7719 (t0) cc_final: 0.6940 (t0) REVERT: F 91 THR cc_start: 0.8742 (p) cc_final: 0.8351 (p) REVERT: G 427 TRP cc_start: 0.7304 (m-10) cc_final: 0.6402 (m-90) REVERT: I 607 ASN cc_start: 0.8264 (m-40) cc_final: 0.7899 (m110) REVERT: I 650 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7687 (tm-30) REVERT: I 656 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6661 (m110) REVERT: J 23 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7929 (pttm) REVERT: J 81 MET cc_start: 0.7306 (mtt) cc_final: 0.7060 (mtt) REVERT: J 110 THR cc_start: 0.7343 (m) cc_final: 0.7124 (m) outliers start: 56 outliers final: 41 residues processed: 310 average time/residue: 0.1398 time to fit residues: 66.5249 Evaluate side-chains 300 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 530 MET Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 641 ILE Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 19 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 223 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 348 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN J 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.092978 restraints weight = 33763.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.095538 restraints weight = 21916.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097290 restraints weight = 16208.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098398 restraints weight = 13095.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099331 restraints weight = 11305.480| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.4945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19359 Z= 0.194 Angle : 0.640 7.245 26421 Z= 0.327 Chirality : 0.045 0.157 3126 Planarity : 0.004 0.036 3243 Dihedral : 5.267 33.563 3723 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.60 % Allowed : 16.12 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2265 helix: 0.59 (0.29), residues: 345 sheet: 0.22 (0.18), residues: 825 loop : -0.40 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 56 TYR 0.016 0.002 TYR D 586 PHE 0.019 0.002 PHE C 376 TRP 0.016 0.002 TRP G 479 HIS 0.003 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00454 (19257) covalent geometry : angle 0.61921 (26157) SS BOND : bond 0.00333 ( 42) SS BOND : angle 0.91006 ( 84) hydrogen bonds : bond 0.04458 ( 672) hydrogen bonds : angle 5.52571 ( 1800) link_BETA1-4 : bond 0.00505 ( 18) link_BETA1-4 : angle 1.56428 ( 54) link_NAG-ASN : bond 0.00342 ( 42) link_NAG-ASN : angle 2.14156 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 271 time to evaluate : 0.681 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 102 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7082 (tm-30) REVERT: A 376 PHE cc_start: 0.7720 (t80) cc_final: 0.7505 (t80) REVERT: B 535 MET cc_start: 0.7322 (mmm) cc_final: 0.6236 (mmp) REVERT: B 545 LEU cc_start: 0.8745 (mt) cc_final: 0.8492 (mt) REVERT: B 649 SER cc_start: 0.9232 (m) cc_final: 0.8974 (t) REVERT: B 650 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: C 39 TYR cc_start: 0.8521 (m-80) cc_final: 0.7886 (m-10) REVERT: C 427 TRP cc_start: 0.8556 (m100) cc_final: 0.8253 (m100) REVERT: D 542 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8055 (ttm110) REVERT: D 593 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7681 (mp) REVERT: D 648 GLU cc_start: 0.8909 (mm-30) cc_final: 0.7991 (pt0) REVERT: D 649 SER cc_start: 0.9228 (m) cc_final: 0.9013 (t) REVERT: D 656 ASN cc_start: 0.7866 (t0) cc_final: 0.7055 (t0) REVERT: F 91 THR cc_start: 0.8692 (p) cc_final: 0.8292 (p) REVERT: I 607 ASN cc_start: 0.8429 (m-40) cc_final: 0.8019 (m110) REVERT: I 650 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: I 656 ASN cc_start: 0.7152 (OUTLIER) cc_final: 0.6533 (m110) REVERT: J 81 MET cc_start: 0.7708 (mtt) cc_final: 0.7411 (mtt) REVERT: K 69 THR cc_start: 0.8428 (p) cc_final: 0.8096 (p) outliers start: 52 outliers final: 42 residues processed: 302 average time/residue: 0.1470 time to fit residues: 67.2341 Evaluate side-chains 296 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 250 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 650 GLN Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 70 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 181 optimal weight: 6.9990 chunk 185 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.094811 restraints weight = 33505.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097377 restraints weight = 21598.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099144 restraints weight = 15964.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100371 restraints weight = 12854.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.101087 restraints weight = 11013.898| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19359 Z= 0.143 Angle : 0.619 9.025 26421 Z= 0.314 Chirality : 0.045 0.160 3126 Planarity : 0.004 0.035 3243 Dihedral : 5.132 37.072 3723 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.60 % Allowed : 16.87 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2265 helix: 0.63 (0.29), residues: 345 sheet: 0.20 (0.18), residues: 834 loop : -0.40 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.024 0.001 TYR D 643 PHE 0.015 0.002 PHE L 98 TRP 0.023 0.001 TRP B 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00327 (19257) covalent geometry : angle 0.60031 (26157) SS BOND : bond 0.00236 ( 42) SS BOND : angle 0.81069 ( 84) hydrogen bonds : bond 0.04185 ( 672) hydrogen bonds : angle 5.47748 ( 1800) link_BETA1-4 : bond 0.00538 ( 18) link_BETA1-4 : angle 1.44541 ( 54) link_NAG-ASN : bond 0.00266 ( 42) link_NAG-ASN : angle 2.04174 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6999 (tm-30) REVERT: B 535 MET cc_start: 0.7240 (mmm) cc_final: 0.5928 (mmp) REVERT: B 545 LEU cc_start: 0.8758 (mt) cc_final: 0.8495 (mt) REVERT: B 610 TRP cc_start: 0.8152 (t-100) cc_final: 0.7823 (t-100) REVERT: B 626 MET cc_start: 0.7790 (mtt) cc_final: 0.7513 (mtt) REVERT: B 649 SER cc_start: 0.9223 (m) cc_final: 0.9022 (t) REVERT: B 650 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: C 39 TYR cc_start: 0.8463 (m-80) cc_final: 0.7810 (m-10) REVERT: C 427 TRP cc_start: 0.8536 (m100) cc_final: 0.8279 (m100) REVERT: D 542 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8231 (tpp80) REVERT: D 593 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7716 (mp) REVERT: D 634 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8420 (mm-30) REVERT: D 648 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8032 (pt0) REVERT: D 651 ASN cc_start: 0.6075 (p0) cc_final: 0.5836 (p0) REVERT: D 656 ASN cc_start: 0.7861 (t0) cc_final: 0.7004 (t0) REVERT: F 91 THR cc_start: 0.8723 (p) cc_final: 0.8331 (p) REVERT: I 607 ASN cc_start: 0.8392 (m-40) cc_final: 0.7994 (m110) REVERT: I 634 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8584 (mm-30) REVERT: I 656 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.6841 (m110) REVERT: J 81 MET cc_start: 0.7765 (mtt) cc_final: 0.7489 (mtt) REVERT: K 69 THR cc_start: 0.8366 (p) cc_final: 0.8027 (p) outliers start: 52 outliers final: 41 residues processed: 302 average time/residue: 0.1363 time to fit residues: 63.0299 Evaluate side-chains 297 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 221 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 115 optimal weight: 0.0070 chunk 168 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.096438 restraints weight = 33294.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.098844 restraints weight = 21143.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.099864 restraints weight = 15411.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100638 restraints weight = 13150.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100857 restraints weight = 12001.910| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19359 Z= 0.129 Angle : 0.622 13.173 26421 Z= 0.314 Chirality : 0.044 0.157 3126 Planarity : 0.004 0.044 3243 Dihedral : 5.041 38.192 3723 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.40 % Allowed : 17.37 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2265 helix: 0.67 (0.29), residues: 345 sheet: 0.26 (0.18), residues: 834 loop : -0.43 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 56 TYR 0.033 0.001 TYR D 643 PHE 0.015 0.001 PHE F 98 TRP 0.048 0.002 TRP I 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00293 (19257) covalent geometry : angle 0.60336 (26157) SS BOND : bond 0.00378 ( 42) SS BOND : angle 1.23858 ( 84) hydrogen bonds : bond 0.04012 ( 672) hydrogen bonds : angle 5.40833 ( 1800) link_BETA1-4 : bond 0.00550 ( 18) link_BETA1-4 : angle 1.35702 ( 54) link_NAG-ASN : bond 0.00252 ( 42) link_NAG-ASN : angle 1.95978 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6901 (tm-30) REVERT: B 535 MET cc_start: 0.7264 (mmm) cc_final: 0.6101 (mmp) REVERT: B 545 LEU cc_start: 0.8788 (mt) cc_final: 0.8551 (mt) REVERT: B 607 ASN cc_start: 0.8527 (m110) cc_final: 0.7889 (m-40) REVERT: B 626 MET cc_start: 0.7649 (mtt) cc_final: 0.7133 (mtp) REVERT: B 649 SER cc_start: 0.9395 (m) cc_final: 0.9078 (t) REVERT: B 650 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: D 542 ARG cc_start: 0.8599 (ttp-170) cc_final: 0.8210 (tpp80) REVERT: D 593 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7732 (mp) REVERT: D 607 ASN cc_start: 0.8414 (m-40) cc_final: 0.7923 (m-40) REVERT: D 610 TRP cc_start: 0.8110 (t-100) cc_final: 0.7727 (t-100) REVERT: D 634 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8371 (mm-30) REVERT: D 656 ASN cc_start: 0.7859 (t0) cc_final: 0.7056 (t0) REVERT: F 91 THR cc_start: 0.8721 (p) cc_final: 0.8333 (p) REVERT: I 542 ARG cc_start: 0.8400 (ttm170) cc_final: 0.7970 (ttm110) REVERT: I 607 ASN cc_start: 0.8415 (m-40) cc_final: 0.8029 (m110) REVERT: I 617 ARG cc_start: 0.7296 (mtp-110) cc_final: 0.7075 (mtp-110) REVERT: I 634 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8600 (mm-30) REVERT: I 656 ASN cc_start: 0.7963 (OUTLIER) cc_final: 0.7308 (m110) REVERT: J 23 LYS cc_start: 0.8102 (ptpt) cc_final: 0.7746 (ptmt) REVERT: J 81 MET cc_start: 0.7694 (mtt) cc_final: 0.7443 (mtt) REVERT: K 69 THR cc_start: 0.8339 (p) cc_final: 0.8004 (p) REVERT: K 91 THR cc_start: 0.8865 (p) cc_final: 0.8662 (p) outliers start: 48 outliers final: 41 residues processed: 312 average time/residue: 0.1351 time to fit residues: 64.9590 Evaluate side-chains 305 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 84 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 69 optimal weight: 0.3980 chunk 219 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.117264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096741 restraints weight = 33112.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099035 restraints weight = 21570.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100248 restraints weight = 15469.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.100886 restraints weight = 12771.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.101099 restraints weight = 12014.454| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19359 Z= 0.142 Angle : 0.635 19.004 26421 Z= 0.319 Chirality : 0.045 0.198 3126 Planarity : 0.004 0.034 3243 Dihedral : 4.999 35.248 3723 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.40 % Allowed : 17.57 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.18), residues: 2265 helix: 0.75 (0.30), residues: 348 sheet: 0.37 (0.19), residues: 810 loop : -0.49 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.023 0.002 TYR B 643 PHE 0.014 0.002 PHE F 98 TRP 0.089 0.002 TRP I 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00327 (19257) covalent geometry : angle 0.61724 (26157) SS BOND : bond 0.00248 ( 42) SS BOND : angle 1.20010 ( 84) hydrogen bonds : bond 0.04082 ( 672) hydrogen bonds : angle 5.38114 ( 1800) link_BETA1-4 : bond 0.00554 ( 18) link_BETA1-4 : angle 1.34249 ( 54) link_NAG-ASN : bond 0.00261 ( 42) link_NAG-ASN : angle 1.93794 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4530 Ramachandran restraints generated. 2265 Oldfield, 0 Emsley, 2265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6930 (tm-30) REVERT: B 535 MET cc_start: 0.7213 (mmm) cc_final: 0.5995 (mmp) REVERT: B 601 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8708 (mtpp) REVERT: B 607 ASN cc_start: 0.8516 (m110) cc_final: 0.7892 (m-40) REVERT: B 649 SER cc_start: 0.9406 (m) cc_final: 0.9128 (t) REVERT: B 650 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: D 542 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8210 (tpp80) REVERT: D 593 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7780 (mp) REVERT: D 607 ASN cc_start: 0.8344 (m-40) cc_final: 0.7879 (m110) REVERT: D 610 TRP cc_start: 0.8068 (t-100) cc_final: 0.7654 (t-100) REVERT: D 634 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8326 (mm-30) REVERT: D 656 ASN cc_start: 0.7844 (t0) cc_final: 0.7024 (t0) REVERT: F 91 THR cc_start: 0.8724 (p) cc_final: 0.8340 (p) REVERT: I 607 ASN cc_start: 0.8379 (m-40) cc_final: 0.8028 (m-40) REVERT: I 617 ARG cc_start: 0.7281 (mtp-110) cc_final: 0.7061 (mtp-110) REVERT: I 656 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7166 (m110) REVERT: J 81 MET cc_start: 0.7701 (mtt) cc_final: 0.7447 (mtt) REVERT: K 69 THR cc_start: 0.8370 (p) cc_final: 0.8028 (p) outliers start: 48 outliers final: 43 residues processed: 298 average time/residue: 0.1383 time to fit residues: 63.0996 Evaluate side-chains 302 residues out of total 1998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 256 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 27 PHE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 98 PHE Chi-restraints excluded: chain C residue 49 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 251 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 569 THR Chi-restraints excluded: chain D residue 593 LEU Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 619 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 98 PHE Chi-restraints excluded: chain G residue 271 MET Chi-restraints excluded: chain G residue 426 MET Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 528 SER Chi-restraints excluded: chain I residue 587 LEU Chi-restraints excluded: chain I residue 619 LEU Chi-restraints excluded: chain I residue 626 MET Chi-restraints excluded: chain I residue 656 ASN Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 98 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 144 optimal weight: 0.0670 chunk 63 optimal weight: 4.9990 chunk 206 optimal weight: 0.5980 chunk 145 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 591 GLN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN D 637 ASN F 24 GLN F 38 GLN F 70 GLN ** G 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 637 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.117685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097228 restraints weight = 33327.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.099610 restraints weight = 21611.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100839 restraints weight = 15476.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101548 restraints weight = 12660.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.101768 restraints weight = 11846.779| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19359 Z= 0.126 Angle : 0.614 9.879 26421 Z= 0.310 Chirality : 0.044 0.168 3126 Planarity : 0.004 0.034 3243 Dihedral : 4.893 32.495 3723 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.30 % Allowed : 17.72 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 2265 helix: 0.23 (0.28), residues: 387 sheet: 0.44 (0.19), residues: 783 loop : -0.48 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 151 TYR 0.030 0.002 TYR D 643 PHE 0.013 0.001 PHE F 98 TRP 0.086 0.002 TRP I 628 HIS 0.003 0.001 HIS G 249 Details of bonding type rmsd covalent geometry : bond 0.00285 (19257) covalent geometry : angle 0.59674 (26157) SS BOND : bond 0.00254 ( 42) SS BOND : angle 1.08101 ( 84) hydrogen bonds : bond 0.03975 ( 672) hydrogen bonds : angle 5.33094 ( 1800) link_BETA1-4 : bond 0.00546 ( 18) link_BETA1-4 : angle 1.27959 ( 54) link_NAG-ASN : bond 0.00242 ( 42) link_NAG-ASN : angle 1.88019 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.99 seconds wall clock time: 50 minutes 59.32 seconds (3059.32 seconds total)