Starting phenix.real_space_refine on Sat Jun 21 10:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.map" model { file = "/net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mi0_48283/06_2025/9mi0_48283.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 153 5.16 5 C 15672 2.51 5 N 4269 2.21 5 O 4908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25002 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3561 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 23, 'TRANS': 427} Chain breaks: 1 Chain: "B" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "C" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3561 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 23, 'TRANS': 427} Chain breaks: 1 Chain: "D" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "P" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 97} Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3561 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 23, 'TRANS': 427} Chain breaks: 1 Chain: "F" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 997 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "S" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "b" 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: "c" 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: "d" 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: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "f" 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: "g" 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" 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: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" 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 Time building chain proxies: 17.50, per 1000 atoms: 0.70 Number of scatterers: 25002 At special positions: 0 Unit cell: (141.644, 153.017, 146.814, 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 153 16.00 O 4908 8.00 N 4269 7.00 C 15672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=1.32 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.36 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.23 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=1.32 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.36 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.23 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=1.32 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.36 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.23 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA U 3 " - " MAN U 4 " " BMA Z 3 " - " MAN Z 4 " " BMA e 3 " - " MAN e 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 339 " " NAG A 606 " - " ASN A 363 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 611 " " NAG C 601 " - " ASN C 160 " " NAG C 602 " - " ASN C 88 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 363 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 160 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 339 " " NAG E 606 " - " ASN E 363 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 234 " " NAG W 1 " - " ASN A 332 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 234 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN E 156 " " NAG d 1 " - " ASN E 392 " " NAG e 1 " - " ASN E 262 " " NAG f 1 " - " ASN E 234 " " NAG g 1 " - " ASN E 332 " Time building additional restraints: 6.41 Conformation dependent library (CDL) restraints added in 3.1 seconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 60 sheets defined 17.0% alpha, 36.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.87 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.028A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.739A pdb=" N PHE G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.902A pdb=" N LYS G 64 " --> pdb=" O ASP G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.625A pdb=" N ASP G 86 " --> pdb=" O ARG G 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR G 87 " --> pdb=" O ASP G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.918A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.643A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.536A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 474 through 478 removed outlier: 3.513A pdb=" N ASP A 477 " --> pdb=" O ASP A 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.728A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 648 removed outlier: 3.688A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 663 removed outlier: 3.509A pdb=" N GLN B 652 " --> pdb=" O GLU B 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'N' and resid 79 through 83 removed outlier: 4.029A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.739A pdb=" N PHE J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.902A pdb=" N LYS J 64 " --> pdb=" O ASP J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.625A pdb=" N ASP J 86 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR J 87 " --> pdb=" O ASP J 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 83 through 87' Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.918A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.643A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.536A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 474 through 478 removed outlier: 3.513A pdb=" N ASP C 477 " --> pdb=" O ASP C 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.728A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 636 Processing helix chain 'D' and resid 638 through 648 removed outlier: 3.688A pdb=" N GLU D 648 " --> pdb=" O GLY D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 663 removed outlier: 3.509A pdb=" N GLN D 652 " --> pdb=" O GLU D 648 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 64 Processing helix chain 'R' and resid 79 through 83 removed outlier: 4.029A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.739A pdb=" N PHE O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 removed outlier: 3.903A pdb=" N LYS O 64 " --> pdb=" O ASP O 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 61 through 64' Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.626A pdb=" N ASP O 86 " --> pdb=" O ARG O 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR O 87 " --> pdb=" O ASP O 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 83 through 87' Processing helix chain 'Q' and resid 79 through 83 Processing helix chain 'E' and resid 57 through 64 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.918A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.643A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.536A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 474 through 478 removed outlier: 3.513A pdb=" N ASP E 477 " --> pdb=" O ASP E 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.728A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 595 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 648 removed outlier: 3.688A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 663 removed outlier: 3.508A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.789A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.446A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.593A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.593A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.606A pdb=" N THR I 105 " --> pdb=" O VAL I 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 18 through 24 Processing sheet with id=AB2, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.487A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.327A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.898A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.282A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.265A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.265A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 305 through 308 Processing sheet with id=AC3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.789A pdb=" N GLU K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA K 88 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AC6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.447A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 10 through 13 Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.594A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.594A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N MET J 34 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 9 through 12 removed outlier: 3.606A pdb=" N THR M 105 " --> pdb=" O VAL M 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 18 through 24 Processing sheet with id=AD4, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.488A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.327A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.898A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD8, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AD9, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AE1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.282A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.264A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 305 through 308 Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'P' and resid 10 through 12 removed outlier: 6.788A pdb=" N GLU P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N MET P 34 " --> pdb=" O TRP P 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP P 50 " --> pdb=" O MET P 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP P 36 " --> pdb=" O MET P 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 4 through 5 Processing sheet with id=AE8, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.447A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 10 through 13 Processing sheet with id=AF1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.594A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE O 102 " --> pdb=" O THR O 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.594A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LEU O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET O 34 " --> pdb=" O LEU O 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 9 through 12 removed outlier: 3.606A pdb=" N THR Q 105 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 18 through 24 Processing sheet with id=AF6, first strand: chain 'Q' and resid 45 through 48 removed outlier: 6.488A pdb=" N TRP Q 35 " --> pdb=" O MET Q 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.327A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.898A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AG1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AG2, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AG3, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.636A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.282A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.265A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU E 381 " --> pdb=" O CYS E 378 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 271 through 273 removed outlier: 11.265A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.967A pdb=" N PHE E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.996A pdb=" N ILE E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N THR E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLY E 451 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 305 through 308 957 hydrogen bonds defined for protein. 2547 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: 10.53 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7948 1.34 - 1.47: 6632 1.47 - 1.60: 10749 1.60 - 1.72: 0 1.72 - 1.85: 216 Bond restraints: 25545 Sorted by residual: bond pdb=" N VAL L 28 " pdb=" CA VAL L 28 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.50e+01 bond pdb=" N VAL N 28 " pdb=" CA VAL N 28 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.50e-03 1.11e+04 1.48e+01 bond pdb=" N VAL R 28 " pdb=" CA VAL R 28 " ideal model delta sigma weight residual 1.456 1.493 -0.036 9.50e-03 1.11e+04 1.47e+01 bond pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.10e+00 bond pdb=" N VAL E 44 " pdb=" CA VAL E 44 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 9.03e+00 ... (remaining 25540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 33083 2.13 - 4.25: 1199 4.25 - 6.38: 301 6.38 - 8.51: 70 8.51 - 10.63: 6 Bond angle restraints: 34659 Sorted by residual: angle pdb=" N VAL L 28 " pdb=" CA VAL L 28 " pdb=" C VAL L 28 " ideal model delta sigma weight residual 113.53 107.22 6.31 9.80e-01 1.04e+00 4.15e+01 angle pdb=" N VAL N 28 " pdb=" CA VAL N 28 " pdb=" C VAL N 28 " ideal model delta sigma weight residual 113.53 107.23 6.30 9.80e-01 1.04e+00 4.13e+01 angle pdb=" N VAL R 28 " pdb=" CA VAL R 28 " pdb=" C VAL R 28 " ideal model delta sigma weight residual 113.53 107.23 6.30 9.80e-01 1.04e+00 4.13e+01 angle pdb=" C ASN A 67 " pdb=" CA ASN A 67 " pdb=" CB ASN A 67 " ideal model delta sigma weight residual 109.65 117.55 -7.90 1.75e+00 3.27e-01 2.04e+01 angle pdb=" C ASN C 67 " pdb=" CA ASN C 67 " pdb=" CB ASN C 67 " ideal model delta sigma weight residual 109.65 117.54 -7.89 1.75e+00 3.27e-01 2.03e+01 ... (remaining 34654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.44: 14195 19.44 - 38.87: 1300 38.87 - 58.31: 318 58.31 - 77.74: 102 77.74 - 97.18: 78 Dihedral angle restraints: 15993 sinusoidal: 7119 harmonic: 8874 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 163.25 -70.25 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 163.24 -70.24 1 1.00e+01 1.00e-02 6.35e+01 ... (remaining 15990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3275 0.061 - 0.122: 563 0.122 - 0.183: 124 0.183 - 0.244: 13 0.244 - 0.305: 6 Chirality restraints: 3981 Sorted by residual: chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.98e+00 chirality pdb=" C1 BMA e 3 " pdb=" O4 NAG e 2 " pdb=" C2 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.73e+00 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.38e+00 ... (remaining 3978 not shown) Planarity restraints: 4404 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG N 24 " -0.938 9.50e-02 1.11e+02 4.21e-01 1.07e+02 pdb=" NE ARG N 24 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG N 24 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG N 24 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG N 24 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 24 " 0.938 9.50e-02 1.11e+02 4.20e-01 1.07e+02 pdb=" NE ARG L 24 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG L 24 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG L 24 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG L 24 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 24 " 0.937 9.50e-02 1.11e+02 4.20e-01 1.07e+02 pdb=" NE ARG R 24 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG R 24 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG R 24 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG R 24 " 0.022 2.00e-02 2.50e+03 ... (remaining 4401 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 213 2.60 - 3.18: 19874 3.18 - 3.75: 37585 3.75 - 4.33: 56888 4.33 - 4.90: 93826 Nonbonded interactions: 208386 Sorted by model distance: nonbonded pdb=" OG1 THR E 37 " pdb=" OG1 THR E 499 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.029 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.030 3.040 nonbonded pdb=" OD2 ASP P 72 " pdb=" OG SER P 74 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP K 72 " pdb=" OG SER K 74 " model vdw 2.226 3.040 ... (remaining 208381 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'U' selection = chain 'Z' selection = chain 'e' } 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 individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 61.410 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.180 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 : 0.010 0.711 25650 Z= 0.501 Angle : 1.160 47.347 34929 Z= 0.577 Chirality : 0.052 0.305 3981 Planarity : 0.015 0.421 4365 Dihedral : 17.436 97.178 10182 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 17.49 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3051 helix: -0.39 (0.23), residues: 441 sheet: -0.50 (0.16), residues: 1020 loop : -0.70 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 112 HIS 0.008 0.002 HIS C 374 PHE 0.013 0.002 PHE E 53 TYR 0.021 0.001 TYR E 217 ARG 0.018 0.002 ARG K 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00494 ( 39) link_NAG-ASN : angle 2.36727 ( 117) link_BETA1-4 : bond 0.00475 ( 18) link_BETA1-4 : angle 2.37565 ( 54) link_ALPHA1-3 : bond 0.01120 ( 3) link_ALPHA1-3 : angle 1.54320 ( 9) hydrogen bonds : bond 0.17672 ( 888) hydrogen bonds : angle 7.83835 ( 2547) SS BOND : bond 0.20862 ( 45) SS BOND : angle 11.27642 ( 90) covalent geometry : bond 0.00523 (25545) covalent geometry : angle 0.99918 (34659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 2.639 Fit side-chains REVERT: I 42 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7840 (ptmt) REVERT: A 82 GLN cc_start: 0.8322 (mm-40) cc_final: 0.8075 (mp10) REVERT: A 166 ARG cc_start: 0.6755 (mmm-85) cc_final: 0.6467 (mmm160) REVERT: A 192 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7167 (ttp-170) REVERT: A 347 LYS cc_start: 0.8347 (ttpp) cc_final: 0.7748 (pttp) REVERT: A 440 GLN cc_start: 0.7904 (mt0) cc_final: 0.7608 (mp10) REVERT: A 479 TRP cc_start: 0.7439 (m-10) cc_final: 0.6581 (m-10) REVERT: B 535 MET cc_start: 0.8660 (mtp) cc_final: 0.8242 (mtm) REVERT: K 53 LYS cc_start: 0.8728 (tttm) cc_final: 0.8523 (mttt) REVERT: N 79 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6129 (mt-10) REVERT: M 42 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7804 (ptmt) REVERT: C 82 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7984 (mp10) REVERT: C 95 MET cc_start: 0.8969 (ttt) cc_final: 0.8646 (ttt) REVERT: C 271 MET cc_start: 0.9006 (mmm) cc_final: 0.8708 (mmp) REVERT: C 347 LYS cc_start: 0.8336 (ttpp) cc_final: 0.7751 (pttp) REVERT: D 538 THR cc_start: 0.8815 (m) cc_final: 0.8546 (p) REVERT: D 633 LYS cc_start: 0.7867 (mttt) cc_final: 0.7364 (mtpt) REVERT: R 61 ARG cc_start: 0.6706 (ptt-90) cc_final: 0.6334 (ptt-90) REVERT: R 79 GLU cc_start: 0.6100 (mt-10) cc_final: 0.5810 (mt-10) REVERT: Q 26 THR cc_start: 0.7967 (p) cc_final: 0.7738 (t) REVERT: E 82 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8097 (mp10) REVERT: E 479 TRP cc_start: 0.7640 (m-10) cc_final: 0.7427 (m-10) REVERT: F 633 LYS cc_start: 0.7879 (mttt) cc_final: 0.7334 (mtmp) outliers start: 0 outliers final: 1 residues processed: 428 average time/residue: 1.7346 time to fit residues: 861.2534 Evaluate side-chains 365 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 237 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 0.0770 chunk 176 optimal weight: 0.1980 chunk 275 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100BGLN G 105 GLN I 37 GLN A 295 ASN A 348 GLN A 377 ASN B 616 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN K 64 GLN J 81 GLN J 100BGLN J 105 GLN M 37 GLN C 295 ASN C 348 GLN C 377 ASN D 607 ASN P 61 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100BGLN O 105 GLN Q 37 GLN E 295 ASN E 348 GLN E 377 ASN F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.194450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156930 restraints weight = 25068.740| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.35 r_work: 0.3457 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 25650 Z= 0.153 Angle : 0.741 15.521 34929 Z= 0.357 Chirality : 0.050 0.668 3981 Planarity : 0.004 0.042 4365 Dihedral : 11.344 89.461 4601 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.14 % Allowed : 17.72 % Favored : 80.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3051 helix: 0.03 (0.24), residues: 462 sheet: -0.27 (0.16), residues: 1023 loop : -0.41 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 112 HIS 0.006 0.001 HIS K 35 PHE 0.017 0.001 PHE E 383 TYR 0.013 0.001 TYR L 91 ARG 0.006 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.01033 ( 39) link_NAG-ASN : angle 2.89696 ( 117) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 2.58373 ( 54) link_ALPHA1-3 : bond 0.00842 ( 3) link_ALPHA1-3 : angle 1.81183 ( 9) hydrogen bonds : bond 0.04735 ( 888) hydrogen bonds : angle 5.73139 ( 2547) SS BOND : bond 0.00613 ( 45) SS BOND : angle 2.61249 ( 90) covalent geometry : bond 0.00342 (25545) covalent geometry : angle 0.70460 (34659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 374 time to evaluate : 2.610 Fit side-chains REVERT: G 46 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: A 82 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8096 (mp10) REVERT: A 192 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7201 (ttp-170) REVERT: A 347 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7751 (pttp) REVERT: A 440 GLN cc_start: 0.7972 (mt0) cc_final: 0.7631 (mp10) REVERT: A 504 ARG cc_start: 0.6674 (tpp-160) cc_final: 0.6319 (tpp-160) REVERT: B 535 MET cc_start: 0.8803 (mtp) cc_final: 0.8367 (mtm) REVERT: K 80 MET cc_start: 0.9044 (tmm) cc_final: 0.8798 (tmt) REVERT: K 105 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7107 (mmp-170) REVERT: C 82 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8050 (mp10) REVERT: C 271 MET cc_start: 0.9000 (mmm) cc_final: 0.8679 (mmp) REVERT: C 347 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7892 (pttp) REVERT: C 372 THR cc_start: 0.8345 (p) cc_final: 0.8121 (p) REVERT: C 426 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8557 (mmt) REVERT: C 479 TRP cc_start: 0.7551 (m-10) cc_final: 0.7060 (m-10) REVERT: C 504 ARG cc_start: 0.6610 (tpp-160) cc_final: 0.6327 (tpp-160) REVERT: D 538 THR cc_start: 0.8919 (m) cc_final: 0.8666 (p) REVERT: D 633 LYS cc_start: 0.8028 (mttt) cc_final: 0.7458 (mtpt) REVERT: R 82 ASP cc_start: 0.5332 (m-30) cc_final: 0.5040 (m-30) REVERT: Q 26 THR cc_start: 0.8157 (p) cc_final: 0.7852 (t) REVERT: E 82 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8003 (mp10) REVERT: E 97 LYS cc_start: 0.8971 (mttm) cc_final: 0.8724 (mttt) REVERT: E 347 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7897 (pttp) REVERT: E 504 ARG cc_start: 0.6466 (tpp-160) cc_final: 0.6192 (tpp-160) REVERT: F 633 LYS cc_start: 0.7930 (mttt) cc_final: 0.7218 (mtmt) REVERT: F 659 ASP cc_start: 0.8016 (t0) cc_final: 0.7280 (t0) outliers start: 57 outliers final: 24 residues processed: 412 average time/residue: 1.3902 time to fit residues: 663.8898 Evaluate side-chains 372 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 345 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 446 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 25 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 124 optimal weight: 8.9990 chunk 282 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN H 64 GLN H 97 HIS ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 114 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN B 616 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 377 ASN F 616 ASN F 650 GLN F 658 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.182325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.143193 restraints weight = 24903.208| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.99 r_work: 0.3295 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 25650 Z= 0.295 Angle : 0.828 13.940 34929 Z= 0.407 Chirality : 0.050 0.301 3981 Planarity : 0.006 0.055 4365 Dihedral : 9.137 76.799 4601 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.16 % Allowed : 17.27 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3051 helix: -0.24 (0.24), residues: 453 sheet: -0.34 (0.16), residues: 1011 loop : -0.50 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 112 HIS 0.007 0.002 HIS K 35 PHE 0.021 0.002 PHE E 383 TYR 0.022 0.002 TYR I 96 ARG 0.007 0.001 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00876 ( 39) link_NAG-ASN : angle 3.17725 ( 117) link_BETA1-4 : bond 0.00674 ( 18) link_BETA1-4 : angle 2.52710 ( 54) link_ALPHA1-3 : bond 0.00780 ( 3) link_ALPHA1-3 : angle 1.65891 ( 9) hydrogen bonds : bond 0.05679 ( 888) hydrogen bonds : angle 5.72514 ( 2547) SS BOND : bond 0.00556 ( 45) SS BOND : angle 2.39301 ( 90) covalent geometry : bond 0.00687 (25545) covalent geometry : angle 0.79507 (34659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 358 time to evaluate : 2.786 Fit side-chains REVERT: G 46 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: A 82 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8213 (mp10) REVERT: A 192 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7767 (ttp-110) REVERT: A 347 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7942 (pttp) REVERT: A 440 GLN cc_start: 0.8123 (mt0) cc_final: 0.7789 (mp10) REVERT: B 535 MET cc_start: 0.9010 (mtp) cc_final: 0.8579 (mtm) REVERT: K 69 MET cc_start: 0.8837 (mtt) cc_final: 0.8448 (mtt) REVERT: J 18 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7204 (tt) REVERT: J 23 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7805 (mmm160) REVERT: J 46 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7723 (tm-30) REVERT: C 82 GLN cc_start: 0.8324 (mm-40) cc_final: 0.7960 (mp10) REVERT: C 268 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8142 (mt-10) REVERT: C 271 MET cc_start: 0.9014 (mmm) cc_final: 0.8653 (mmp) REVERT: C 278 ARG cc_start: 0.8962 (mmm160) cc_final: 0.8643 (mmm160) REVERT: C 347 LYS cc_start: 0.8547 (ttpp) cc_final: 0.8060 (pttp) REVERT: C 426 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8627 (mmt) REVERT: D 538 THR cc_start: 0.9049 (m) cc_final: 0.8818 (p) REVERT: D 633 LYS cc_start: 0.8204 (mttt) cc_final: 0.7639 (mtpt) REVERT: D 648 GLU cc_start: 0.5188 (OUTLIER) cc_final: 0.4814 (pm20) REVERT: P 94 ARG cc_start: 0.8415 (ttp-170) cc_final: 0.8177 (tmt170) REVERT: E 82 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8055 (mp10) REVERT: E 97 LYS cc_start: 0.9088 (mttm) cc_final: 0.8804 (mtmt) REVERT: E 150 MET cc_start: 0.6514 (tpt) cc_final: 0.6314 (tpt) REVERT: E 347 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8117 (pttp) REVERT: F 617 ARG cc_start: 0.9018 (mtp85) cc_final: 0.8818 (mtp85) REVERT: F 633 LYS cc_start: 0.7910 (mttt) cc_final: 0.7291 (mtmt) REVERT: F 659 ASP cc_start: 0.8841 (t0) cc_final: 0.8312 (t70) outliers start: 84 outliers final: 46 residues processed: 407 average time/residue: 1.7530 time to fit residues: 821.4490 Evaluate side-chains 387 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 17 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 377 ASN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain N residue 1 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 37 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 269 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN C 377 ASN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 616 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.181774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142168 restraints weight = 25176.516| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.83 r_work: 0.3335 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25650 Z= 0.173 Angle : 0.689 11.484 34929 Z= 0.338 Chirality : 0.046 0.284 3981 Planarity : 0.004 0.045 4365 Dihedral : 8.028 76.201 4601 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 19.19 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3051 helix: -0.01 (0.24), residues: 456 sheet: -0.35 (0.16), residues: 975 loop : -0.41 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 112 HIS 0.004 0.001 HIS A 173 PHE 0.016 0.001 PHE A 383 TYR 0.017 0.001 TYR B 638 ARG 0.012 0.001 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 39) link_NAG-ASN : angle 3.20012 ( 117) link_BETA1-4 : bond 0.00570 ( 18) link_BETA1-4 : angle 2.39748 ( 54) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.69106 ( 9) hydrogen bonds : bond 0.04427 ( 888) hydrogen bonds : angle 5.43522 ( 2547) SS BOND : bond 0.00280 ( 45) SS BOND : angle 2.05476 ( 90) covalent geometry : bond 0.00392 (25545) covalent geometry : angle 0.65022 (34659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 361 time to evaluate : 2.710 Fit side-chains REVERT: H 72 ASP cc_start: 0.8187 (t70) cc_final: 0.7910 (t0) REVERT: G 46 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 82 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8144 (mp10) REVERT: A 192 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7287 (ttp-170) REVERT: A 347 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7768 (pttp) REVERT: A 440 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: A 444 ARG cc_start: 0.7907 (tmt170) cc_final: 0.7546 (tpt170) REVERT: B 535 MET cc_start: 0.8943 (mtp) cc_final: 0.8523 (mtm) REVERT: B 659 ASP cc_start: 0.8595 (t0) cc_final: 0.8128 (t70) REVERT: K 80 MET cc_start: 0.9145 (tmm) cc_final: 0.8817 (tmt) REVERT: J 18 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7203 (tt) REVERT: J 23 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7640 (mmm160) REVERT: C 49 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8787 (mt-10) REVERT: C 82 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8009 (mp10) REVERT: C 268 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 271 MET cc_start: 0.8969 (mmm) cc_final: 0.8612 (mmp) REVERT: C 278 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8549 (mmm160) REVERT: C 321 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6846 (t0) REVERT: C 347 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7821 (pttp) REVERT: C 372 THR cc_start: 0.8316 (p) cc_final: 0.8096 (p) REVERT: C 426 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8645 (mmt) REVERT: C 444 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.6077 (ttt180) REVERT: D 538 THR cc_start: 0.9050 (m) cc_final: 0.8754 (p) REVERT: D 633 LYS cc_start: 0.8115 (mttt) cc_final: 0.7513 (mtpt) REVERT: D 648 GLU cc_start: 0.4032 (OUTLIER) cc_final: 0.3789 (pt0) REVERT: P 66 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7813 (mtm180) REVERT: P 94 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.8129 (tmt170) REVERT: O 46 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8542 (tt0) REVERT: E 82 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7970 (mp10) REVERT: E 97 LYS cc_start: 0.8980 (mttm) cc_final: 0.8677 (mtmt) REVERT: E 347 LYS cc_start: 0.8415 (ttpp) cc_final: 0.7907 (pttp) REVERT: F 633 LYS cc_start: 0.7892 (mttt) cc_final: 0.7161 (mtmt) REVERT: F 659 ASP cc_start: 0.8681 (t0) cc_final: 0.8016 (t70) outliers start: 70 outliers final: 40 residues processed: 401 average time/residue: 1.4624 time to fit residues: 675.5636 Evaluate side-chains 394 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 66 ARG Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 300 optimal weight: 0.9990 chunk 260 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 148 optimal weight: 8.9990 chunk 216 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 46 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN C 377 ASN D 650 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 616 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.180387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132744 restraints weight = 24990.508| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.05 r_work: 0.3309 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 25650 Z= 0.216 Angle : 0.710 11.474 34929 Z= 0.347 Chirality : 0.047 0.345 3981 Planarity : 0.005 0.037 4365 Dihedral : 7.549 76.334 4601 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.75 % Allowed : 19.79 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3051 helix: 0.01 (0.24), residues: 456 sheet: -0.35 (0.15), residues: 999 loop : -0.41 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 112 HIS 0.004 0.001 HIS O 82A PHE 0.017 0.002 PHE E 383 TYR 0.016 0.002 TYR I 96 ARG 0.004 0.000 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 39) link_NAG-ASN : angle 3.54285 ( 117) link_BETA1-4 : bond 0.00620 ( 18) link_BETA1-4 : angle 2.44224 ( 54) link_ALPHA1-3 : bond 0.00692 ( 3) link_ALPHA1-3 : angle 1.65586 ( 9) hydrogen bonds : bond 0.04632 ( 888) hydrogen bonds : angle 5.38769 ( 2547) SS BOND : bond 0.00375 ( 45) SS BOND : angle 2.03080 ( 90) covalent geometry : bond 0.00502 (25545) covalent geometry : angle 0.66657 (34659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 344 time to evaluate : 2.677 Fit side-chains REVERT: H 72 ASP cc_start: 0.8165 (t70) cc_final: 0.7899 (t0) REVERT: G 46 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: A 82 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8078 (mp10) REVERT: A 192 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7229 (ttp-170) REVERT: A 347 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7744 (pttp) REVERT: A 440 GLN cc_start: 0.8022 (mt0) cc_final: 0.7656 (mp10) REVERT: B 535 MET cc_start: 0.8918 (mtp) cc_final: 0.8486 (mtm) REVERT: B 648 GLU cc_start: 0.3746 (OUTLIER) cc_final: 0.3472 (pm20) REVERT: J 23 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7628 (mmm160) REVERT: C 49 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8674 (mt-10) REVERT: C 82 GLN cc_start: 0.8370 (mm-40) cc_final: 0.7946 (mp10) REVERT: C 268 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8015 (mt-10) REVERT: C 271 MET cc_start: 0.8904 (mmm) cc_final: 0.8517 (mmp) REVERT: C 278 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8514 (mmm160) REVERT: C 321 ASP cc_start: 0.7265 (OUTLIER) cc_final: 0.6967 (t0) REVERT: C 347 LYS cc_start: 0.8377 (ttpp) cc_final: 0.7822 (pttp) REVERT: C 372 THR cc_start: 0.8329 (p) cc_final: 0.8121 (p) REVERT: C 426 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8417 (mmt) REVERT: D 538 THR cc_start: 0.8968 (m) cc_final: 0.8664 (p) REVERT: D 659 ASP cc_start: 0.8494 (t0) cc_final: 0.8273 (t70) REVERT: P 64 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7969 (mm110) REVERT: P 94 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7863 (ttt-90) REVERT: O 46 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: E 82 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7943 (mp10) REVERT: E 97 LYS cc_start: 0.8998 (mttm) cc_final: 0.8661 (mtmt) REVERT: E 347 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7914 (pttp) REVERT: F 633 LYS cc_start: 0.7818 (mttt) cc_final: 0.7066 (mtmt) REVERT: F 659 ASP cc_start: 0.8727 (t0) cc_final: 0.8121 (t70) outliers start: 73 outliers final: 47 residues processed: 390 average time/residue: 1.3381 time to fit residues: 604.1646 Evaluate side-chains 386 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 333 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain N residue 1 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 45 LYS Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 290 optimal weight: 0.9980 chunk 246 optimal weight: 0.7980 chunk 294 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100BGLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN C 377 ASN D 650 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.181981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.141692 restraints weight = 24981.829| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.97 r_work: 0.3326 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25650 Z= 0.155 Angle : 0.648 12.333 34929 Z= 0.316 Chirality : 0.045 0.445 3981 Planarity : 0.004 0.037 4365 Dihedral : 7.229 75.464 4601 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.01 % Allowed : 20.13 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3051 helix: 0.22 (0.24), residues: 456 sheet: -0.31 (0.16), residues: 999 loop : -0.30 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 112 HIS 0.004 0.001 HIS A 173 PHE 0.015 0.001 PHE E 383 TYR 0.014 0.001 TYR I 96 ARG 0.003 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 39) link_NAG-ASN : angle 3.60082 ( 117) link_BETA1-4 : bond 0.00568 ( 18) link_BETA1-4 : angle 2.27341 ( 54) link_ALPHA1-3 : bond 0.00740 ( 3) link_ALPHA1-3 : angle 1.56591 ( 9) hydrogen bonds : bond 0.04086 ( 888) hydrogen bonds : angle 5.25862 ( 2547) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.89961 ( 90) covalent geometry : bond 0.00352 (25545) covalent geometry : angle 0.60098 (34659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 347 time to evaluate : 2.836 Fit side-chains REVERT: H 10 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7330 (mt-10) REVERT: H 72 ASP cc_start: 0.8172 (t70) cc_final: 0.7898 (t0) REVERT: G 46 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: I 95 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7488 (p) REVERT: A 82 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8064 (mp10) REVERT: A 192 ARG cc_start: 0.7871 (ttp80) cc_final: 0.7468 (ttp-170) REVERT: A 347 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7784 (pttp) REVERT: A 440 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7615 (mp10) REVERT: A 444 ARG cc_start: 0.7794 (tmt170) cc_final: 0.7400 (tpt170) REVERT: B 535 MET cc_start: 0.8920 (mtp) cc_final: 0.8510 (mtm) REVERT: K 10 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: K 80 MET cc_start: 0.9156 (tmm) cc_final: 0.8858 (tmt) REVERT: J 46 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: C 49 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8686 (mt-10) REVERT: C 82 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8011 (mp10) REVERT: C 268 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8023 (mt-10) REVERT: C 271 MET cc_start: 0.8928 (mmm) cc_final: 0.8554 (mmp) REVERT: C 278 ARG cc_start: 0.8889 (mmm160) cc_final: 0.8551 (mmm160) REVERT: C 347 LYS cc_start: 0.8355 (ttpp) cc_final: 0.7808 (pttp) REVERT: C 426 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: D 538 THR cc_start: 0.8997 (m) cc_final: 0.8666 (p) REVERT: P 10 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: P 64 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7945 (mm110) REVERT: P 94 ARG cc_start: 0.8373 (ttp-170) cc_final: 0.7912 (ttt-90) REVERT: P 98 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7642 (p0) REVERT: O 46 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: Q 95 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.7645 (p) REVERT: E 82 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7937 (mp10) REVERT: E 97 LYS cc_start: 0.8994 (mttm) cc_final: 0.8672 (mtmt) REVERT: E 347 LYS cc_start: 0.8449 (ttpp) cc_final: 0.7942 (pttp) REVERT: F 659 ASP cc_start: 0.8690 (t0) cc_final: 0.7959 (t70) outliers start: 80 outliers final: 41 residues processed: 396 average time/residue: 1.3837 time to fit residues: 632.3815 Evaluate side-chains 387 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 335 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain K residue 10 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN C 377 ASN D 650 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.178223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131830 restraints weight = 25183.285| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.96 r_work: 0.3283 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 25650 Z= 0.301 Angle : 0.791 20.231 34929 Z= 0.385 Chirality : 0.050 0.717 3981 Planarity : 0.005 0.042 4365 Dihedral : 7.476 80.225 4599 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.35 % Allowed : 20.02 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3051 helix: -0.13 (0.24), residues: 456 sheet: -0.47 (0.15), residues: 1014 loop : -0.36 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 112 HIS 0.005 0.001 HIS O 82A PHE 0.019 0.002 PHE A 383 TYR 0.018 0.002 TYR I 96 ARG 0.007 0.001 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 39) link_NAG-ASN : angle 4.30108 ( 117) link_BETA1-4 : bond 0.00533 ( 18) link_BETA1-4 : angle 2.43371 ( 54) link_ALPHA1-3 : bond 0.00526 ( 3) link_ALPHA1-3 : angle 1.81747 ( 9) hydrogen bonds : bond 0.05142 ( 888) hydrogen bonds : angle 5.55944 ( 2547) SS BOND : bond 0.00438 ( 45) SS BOND : angle 2.23689 ( 90) covalent geometry : bond 0.00709 (25545) covalent geometry : angle 0.73789 (34659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 339 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8190 (t70) cc_final: 0.7945 (t0) REVERT: H 82 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: L 1 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7829 (t) REVERT: G 46 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7679 (tm-30) REVERT: I 95 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 82 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8060 (mp10) REVERT: A 192 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7306 (ttp-170) REVERT: A 347 LYS cc_start: 0.8319 (ttpp) cc_final: 0.7752 (pttp) REVERT: A 440 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: A 444 ARG cc_start: 0.7993 (tmt170) cc_final: 0.7589 (tpt170) REVERT: B 535 MET cc_start: 0.8931 (mtp) cc_final: 0.8508 (mtm) REVERT: B 648 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3385 (pt0) REVERT: J 46 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: M 42 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8041 (mtmm) REVERT: C 49 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8740 (mt-10) REVERT: C 82 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8009 (mp10) REVERT: C 268 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8046 (mt-10) REVERT: C 271 MET cc_start: 0.8863 (mmm) cc_final: 0.8504 (mmp) REVERT: C 278 ARG cc_start: 0.8861 (mmm160) cc_final: 0.8529 (mmm160) REVERT: C 347 LYS cc_start: 0.8462 (ttpp) cc_final: 0.7909 (pttp) REVERT: C 426 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8565 (mmt) REVERT: D 538 THR cc_start: 0.9036 (m) cc_final: 0.8696 (p) REVERT: P 10 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7270 (mt-10) REVERT: P 94 ARG cc_start: 0.8369 (ttp-170) cc_final: 0.7872 (ttt-90) REVERT: P 98 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8078 (p0) REVERT: O 46 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8567 (tt0) REVERT: Q 95 THR cc_start: 0.8275 (OUTLIER) cc_final: 0.7579 (p) REVERT: E 82 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7988 (mp10) REVERT: E 97 LYS cc_start: 0.9011 (mttm) cc_final: 0.8671 (mtmt) REVERT: E 444 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7704 (tpt170) REVERT: F 633 LYS cc_start: 0.7830 (mttt) cc_final: 0.7074 (mtmt) REVERT: F 659 ASP cc_start: 0.8826 (t0) cc_final: 0.8299 (t70) outliers start: 89 outliers final: 54 residues processed: 399 average time/residue: 1.4395 time to fit residues: 673.0255 Evaluate side-chains 395 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 330 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 221 optimal weight: 7.9990 chunk 152 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 299 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100BGLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 650 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.180937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.134501 restraints weight = 25140.920| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.93 r_work: 0.3339 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25650 Z= 0.153 Angle : 0.656 13.710 34929 Z= 0.321 Chirality : 0.045 0.453 3981 Planarity : 0.004 0.038 4365 Dihedral : 6.998 78.651 4599 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.86 % Allowed : 20.88 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.15), residues: 3051 helix: 0.17 (0.24), residues: 453 sheet: -0.36 (0.16), residues: 999 loop : -0.24 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 112 HIS 0.003 0.001 HIS A 173 PHE 0.017 0.001 PHE E 376 TYR 0.014 0.001 TYR I 96 ARG 0.004 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 39) link_NAG-ASN : angle 3.95805 ( 117) link_BETA1-4 : bond 0.00530 ( 18) link_BETA1-4 : angle 2.20593 ( 54) link_ALPHA1-3 : bond 0.00655 ( 3) link_ALPHA1-3 : angle 1.51930 ( 9) hydrogen bonds : bond 0.04093 ( 888) hydrogen bonds : angle 5.30281 ( 2547) SS BOND : bond 0.00254 ( 45) SS BOND : angle 1.74884 ( 90) covalent geometry : bond 0.00346 (25545) covalent geometry : angle 0.60339 (34659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 335 time to evaluate : 2.598 Fit side-chains revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8152 (t70) cc_final: 0.7889 (t0) REVERT: H 82 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: G 46 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: I 42 LYS cc_start: 0.8262 (mtmm) cc_final: 0.7992 (ptpt) REVERT: I 95 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 82 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8028 (mp10) REVERT: A 192 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7312 (ttp-170) REVERT: A 347 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7719 (pttp) REVERT: A 440 GLN cc_start: 0.8006 (mt0) cc_final: 0.7628 (mp10) REVERT: A 444 ARG cc_start: 0.8009 (tmt170) cc_final: 0.7548 (tpt170) REVERT: B 535 MET cc_start: 0.8907 (mtp) cc_final: 0.8488 (mtm) REVERT: B 647 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7291 (tm-30) REVERT: K 3 GLN cc_start: 0.8438 (tt0) cc_final: 0.8233 (tt0) REVERT: J 46 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: M 42 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8038 (mtmm) REVERT: C 49 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8573 (mt-10) REVERT: C 82 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7973 (mp10) REVERT: C 268 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7975 (mt-10) REVERT: C 271 MET cc_start: 0.8862 (mmm) cc_final: 0.8509 (mmp) REVERT: C 278 ARG cc_start: 0.8824 (mmm160) cc_final: 0.8486 (mmm160) REVERT: C 347 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7745 (pttp) REVERT: C 426 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (mmt) REVERT: C 444 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7181 (ttt180) REVERT: P 10 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7323 (mt-10) REVERT: P 94 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7871 (ttt-90) REVERT: P 98 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7826 (p0) REVERT: O 46 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8508 (tt0) REVERT: Q 95 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7607 (p) REVERT: E 82 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7975 (mp10) REVERT: E 97 LYS cc_start: 0.8962 (mttm) cc_final: 0.8622 (mtmt) REVERT: E 192 ARG cc_start: 0.7592 (ttp-110) cc_final: 0.7333 (ttp-110) REVERT: E 347 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7871 (pttp) REVERT: F 659 ASP cc_start: 0.8650 (t0) cc_final: 0.7996 (t70) outliers start: 76 outliers final: 53 residues processed: 381 average time/residue: 1.3684 time to fit residues: 601.5417 Evaluate side-chains 388 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 241 optimal weight: 0.0470 chunk 73 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 136 optimal weight: 0.5980 chunk 141 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 650 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.179497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132595 restraints weight = 25233.370| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.88 r_work: 0.3304 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25650 Z= 0.220 Angle : 0.705 15.735 34929 Z= 0.346 Chirality : 0.048 0.700 3981 Planarity : 0.004 0.036 4365 Dihedral : 6.963 80.323 4599 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 20.73 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 3051 helix: 0.16 (0.24), residues: 450 sheet: -0.38 (0.16), residues: 999 loop : -0.25 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 112 HIS 0.004 0.001 HIS A 173 PHE 0.018 0.002 PHE E 383 TYR 0.016 0.002 TYR I 96 ARG 0.004 0.000 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 39) link_NAG-ASN : angle 3.86196 ( 117) link_BETA1-4 : bond 0.00484 ( 18) link_BETA1-4 : angle 2.27419 ( 54) link_ALPHA1-3 : bond 0.00537 ( 3) link_ALPHA1-3 : angle 1.63729 ( 9) hydrogen bonds : bond 0.04539 ( 888) hydrogen bonds : angle 5.38618 ( 2547) SS BOND : bond 0.00336 ( 45) SS BOND : angle 1.86061 ( 90) covalent geometry : bond 0.00515 (25545) covalent geometry : angle 0.65756 (34659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 336 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8184 (t70) cc_final: 0.7930 (t0) REVERT: H 82 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: G 46 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: I 42 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7950 (ptpt) REVERT: I 95 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7593 (p) REVERT: A 82 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8033 (mp10) REVERT: A 192 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7286 (ttp-170) REVERT: A 347 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7752 (pttp) REVERT: A 440 GLN cc_start: 0.8039 (mt0) cc_final: 0.7663 (mp10) REVERT: B 535 MET cc_start: 0.8941 (mtp) cc_final: 0.8509 (mtm) REVERT: K 3 GLN cc_start: 0.8425 (tt0) cc_final: 0.8210 (tt0) REVERT: J 46 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: M 42 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8046 (mtmm) REVERT: C 49 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8642 (mt-10) REVERT: C 82 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7978 (mp10) REVERT: C 268 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8039 (mt-10) REVERT: C 271 MET cc_start: 0.8866 (mmm) cc_final: 0.8505 (mmp) REVERT: C 278 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8518 (mmm160) REVERT: C 347 LYS cc_start: 0.8385 (ttpp) cc_final: 0.7823 (pttp) REVERT: C 444 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7210 (ttt180) REVERT: C 475 MET cc_start: 0.9116 (mmt) cc_final: 0.8914 (mmt) REVERT: P 10 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: P 39 GLN cc_start: 0.8095 (tp40) cc_final: 0.7541 (tt0) REVERT: P 66 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7836 (ttp80) REVERT: P 94 ARG cc_start: 0.8348 (ttp-170) cc_final: 0.7871 (ttt-90) REVERT: P 98 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.7997 (p0) REVERT: O 46 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: Q 95 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7597 (p) REVERT: E 82 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7987 (mp10) REVERT: E 97 LYS cc_start: 0.9004 (mttm) cc_final: 0.8666 (mtmt) REVERT: E 192 ARG cc_start: 0.7634 (ttp-110) cc_final: 0.7376 (ttp-110) REVERT: E 347 LYS cc_start: 0.8452 (ttpp) cc_final: 0.7927 (pttp) REVERT: E 444 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7496 (tpt170) REVERT: F 659 ASP cc_start: 0.8713 (t0) cc_final: 0.8118 (t70) outliers start: 83 outliers final: 60 residues processed: 389 average time/residue: 1.3414 time to fit residues: 601.8884 Evaluate side-chains 397 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 328 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain O residue 11 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 115 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 300 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 238 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 650 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.180996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135033 restraints weight = 25100.895| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.86 r_work: 0.3343 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25650 Z= 0.158 Angle : 0.642 14.245 34929 Z= 0.316 Chirality : 0.045 0.534 3981 Planarity : 0.004 0.036 4365 Dihedral : 6.696 79.019 4599 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.82 % Allowed : 21.22 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.15), residues: 3051 helix: 0.41 (0.26), residues: 429 sheet: -0.32 (0.16), residues: 999 loop : -0.15 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 112 HIS 0.003 0.001 HIS A 173 PHE 0.015 0.001 PHE E 383 TYR 0.014 0.001 TYR I 96 ARG 0.004 0.000 ARG F 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 39) link_NAG-ASN : angle 3.59664 ( 117) link_BETA1-4 : bond 0.00495 ( 18) link_BETA1-4 : angle 2.17635 ( 54) link_ALPHA1-3 : bond 0.00592 ( 3) link_ALPHA1-3 : angle 1.53167 ( 9) hydrogen bonds : bond 0.04073 ( 888) hydrogen bonds : angle 5.25873 ( 2547) SS BOND : bond 0.00271 ( 45) SS BOND : angle 1.60233 ( 90) covalent geometry : bond 0.00361 (25545) covalent geometry : angle 0.59734 (34659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 339 time to evaluate : 2.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8158 (t70) cc_final: 0.7900 (t0) REVERT: H 82 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7544 (mtm-85) REVERT: G 46 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: I 42 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7941 (ptpt) REVERT: I 95 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 82 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7988 (mp10) REVERT: A 192 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7283 (ttp-170) REVERT: A 347 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7727 (pttp) REVERT: A 440 GLN cc_start: 0.8011 (mt0) cc_final: 0.7637 (mp10) REVERT: B 535 MET cc_start: 0.8916 (mtp) cc_final: 0.8492 (mtm) REVERT: B 647 GLU cc_start: 0.6864 (tm-30) cc_final: 0.6661 (tm-30) REVERT: K 3 GLN cc_start: 0.8394 (tt0) cc_final: 0.8174 (tt0) REVERT: J 46 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: M 42 LYS cc_start: 0.8334 (mtmm) cc_final: 0.8066 (mtmm) REVERT: C 49 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8599 (mt-10) REVERT: C 82 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7936 (mp10) REVERT: C 268 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8000 (mt-10) REVERT: C 271 MET cc_start: 0.8864 (mmm) cc_final: 0.8531 (mmp) REVERT: C 278 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8516 (mmm160) REVERT: C 347 LYS cc_start: 0.8330 (ttpp) cc_final: 0.7769 (pttp) REVERT: C 444 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7243 (ttt180) REVERT: D 647 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7223 (tm-30) REVERT: P 10 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: P 39 GLN cc_start: 0.8030 (tp40) cc_final: 0.7469 (tt0) REVERT: P 66 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7822 (ttp80) REVERT: P 94 ARG cc_start: 0.8321 (ttp-170) cc_final: 0.7860 (ttt-90) REVERT: P 98 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.7868 (p0) REVERT: O 46 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8534 (tt0) REVERT: Q 95 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7514 (p) REVERT: E 82 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7921 (mp10) REVERT: E 97 LYS cc_start: 0.8963 (mttm) cc_final: 0.8623 (mtmt) REVERT: E 347 LYS cc_start: 0.8401 (ttpp) cc_final: 0.7861 (pttp) REVERT: E 444 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7461 (tpt170) REVERT: F 659 ASP cc_start: 0.8641 (t0) cc_final: 0.7989 (t70) outliers start: 75 outliers final: 55 residues processed: 386 average time/residue: 1.4078 time to fit residues: 631.3709 Evaluate side-chains 397 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 333 time to evaluate : 2.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 1 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 23 ARG Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain C residue 72 HIS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 464 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 98 ASP Chi-restraints excluded: chain P residue 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 62 SER Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 87 THR Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain O residue 111 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 72 HIS Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 377 ASN Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain F residue 639 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 117 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN D 650 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN E 377 ASN F 653 GLN F 658 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.181165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132212 restraints weight = 25041.142| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.89 r_work: 0.3293 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25650 Z= 0.277 Angle : 0.749 13.805 34929 Z= 0.368 Chirality : 0.049 0.489 3981 Planarity : 0.005 0.039 4365 Dihedral : 6.937 84.648 4599 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.97 % Allowed : 21.26 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3051 helix: 0.09 (0.25), residues: 447 sheet: -0.42 (0.16), residues: 1014 loop : -0.26 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 112 HIS 0.006 0.001 HIS O 82A PHE 0.020 0.002 PHE A 383 TYR 0.018 0.002 TYR I 96 ARG 0.005 0.000 ARG E 503 Details of bonding type rmsd link_NAG-ASN : bond 0.00618 ( 39) link_NAG-ASN : angle 3.81014 ( 117) link_BETA1-4 : bond 0.00491 ( 18) link_BETA1-4 : angle 2.35841 ( 54) link_ALPHA1-3 : bond 0.00456 ( 3) link_ALPHA1-3 : angle 1.73434 ( 9) hydrogen bonds : bond 0.04942 ( 888) hydrogen bonds : angle 5.50068 ( 2547) SS BOND : bond 0.00409 ( 45) SS BOND : angle 1.99205 ( 90) covalent geometry : bond 0.00653 (25545) covalent geometry : angle 0.70481 (34659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21478.52 seconds wall clock time: 372 minutes 23.83 seconds (22343.83 seconds total)