Starting phenix.real_space_refine on Fri Sep 19 09:08:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mi0_48283/09_2025/9mi0_48283.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mi0_48283/09_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_48283/09_2025/9mi0_48283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mi0_48283/09_2025/9mi0_48283.map" model { file = "/net/cci-nas-00/data/ceres_data/9mi0_48283/09_2025/9mi0_48283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mi0_48283/09_2025/9mi0_48283.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 6.40, per 1000 atoms: 0.26 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: 2.18 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.21 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: 6.13 Time building geometry restraints manager: 2.94 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: 0.07 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: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 25.950 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.002 ARG K 83 TYR 0.021 0.001 TYR E 217 PHE 0.013 0.002 PHE E 53 TRP 0.037 0.002 TRP A 112 HIS 0.008 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00523 (25545) covalent geometry : angle 0.99918 (34659) SS BOND : bond 0.20862 ( 45) SS BOND : angle 11.27642 ( 90) hydrogen bonds : bond 0.17672 ( 888) hydrogen bonds : angle 7.83835 ( 2547) link_ALPHA1-3 : bond 0.01120 ( 3) link_ALPHA1-3 : angle 1.54320 ( 9) link_BETA1-4 : bond 0.00475 ( 18) link_BETA1-4 : angle 2.37565 ( 54) link_NAG-ASN : bond 0.00494 ( 39) link_NAG-ASN : angle 2.36727 ( 117) *********************** 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 : 0.948 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: 0.6442 (ptt-90) REVERT: R 79 GLU cc_start: 0.6100 (mt-10) cc_final: 0.5857 (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: 0.6934 time to fit residues: 340.6576 Evaluate side-chains 366 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 365 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.4980 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 61 GLN H 64 GLN ** G 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 105 GLN M 37 GLN C 114 GLN C 295 ASN C 348 GLN C 377 ASN D 607 ASN D 650 GLN P 61 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 105 GLN Q 37 GLN E 114 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 = 0.4083 r_free = 0.4083 target = 0.191789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154046 restraints weight = 25067.410| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.65 r_work: 0.3414 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 25650 Z= 0.184 Angle : 0.779 16.747 34929 Z= 0.376 Chirality : 0.053 0.753 3981 Planarity : 0.005 0.044 4365 Dihedral : 11.433 90.296 4601 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.63 % Allowed : 17.49 % Favored : 79.87 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.14), residues: 3051 helix: -0.01 (0.24), residues: 456 sheet: -0.29 (0.16), residues: 1011 loop : -0.45 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 192 TYR 0.018 0.002 TYR B 638 PHE 0.020 0.002 PHE E 383 TRP 0.023 0.002 TRP E 427 HIS 0.008 0.001 HIS P 35 Details of bonding type rmsd covalent geometry : bond 0.00423 (25545) covalent geometry : angle 0.74313 (34659) SS BOND : bond 0.00301 ( 45) SS BOND : angle 2.70230 ( 90) hydrogen bonds : bond 0.04991 ( 888) hydrogen bonds : angle 5.73540 ( 2547) link_ALPHA1-3 : bond 0.00785 ( 3) link_ALPHA1-3 : angle 1.86467 ( 9) link_BETA1-4 : bond 0.00529 ( 18) link_BETA1-4 : angle 2.59124 ( 54) link_NAG-ASN : bond 0.00815 ( 39) link_NAG-ASN : angle 2.96165 ( 117) *********************** 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 440 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 370 time to evaluate : 0.976 Fit side-chains REVERT: G 46 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: A 82 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8116 (mp10) REVERT: A 192 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7310 (ttp-170) REVERT: A 347 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7801 (pttp) REVERT: A 440 GLN cc_start: 0.8001 (mt0) cc_final: 0.7658 (mp10) REVERT: A 504 ARG cc_start: 0.6760 (tpp-160) cc_final: 0.6405 (tpp-160) REVERT: B 535 MET cc_start: 0.8879 (mtp) cc_final: 0.8424 (mtm) REVERT: K 80 MET cc_start: 0.9051 (tmm) cc_final: 0.8795 (tmt) REVERT: C 82 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7981 (mp10) REVERT: C 95 MET cc_start: 0.9125 (ttt) cc_final: 0.8691 (ttt) REVERT: C 271 MET cc_start: 0.9010 (mmm) cc_final: 0.8634 (mmp) REVERT: C 347 LYS cc_start: 0.8449 (ttpp) cc_final: 0.7967 (pttp) REVERT: C 372 THR cc_start: 0.8352 (p) cc_final: 0.8126 (p) REVERT: C 479 TRP cc_start: 0.7518 (m-10) cc_final: 0.6901 (m-10) REVERT: C 504 ARG cc_start: 0.6692 (tpp-160) cc_final: 0.6433 (tpp-160) REVERT: D 538 THR cc_start: 0.9059 (m) cc_final: 0.8795 (p) REVERT: D 633 LYS cc_start: 0.8061 (mttt) cc_final: 0.7469 (mtpt) REVERT: D 659 ASP cc_start: 0.8405 (t0) cc_final: 0.7856 (t0) REVERT: R 82 ASP cc_start: 0.5190 (m-30) cc_final: 0.4830 (m-30) REVERT: Q 26 THR cc_start: 0.8203 (p) cc_final: 0.7886 (t) REVERT: E 82 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7988 (mp10) REVERT: E 97 LYS cc_start: 0.9035 (mttm) cc_final: 0.8792 (mttt) REVERT: E 192 ARG cc_start: 0.7512 (ttp-170) cc_final: 0.7241 (ttp-110) REVERT: F 633 LYS cc_start: 0.7936 (mttt) cc_final: 0.7226 (mtmt) REVERT: F 659 ASP cc_start: 0.8311 (t0) cc_final: 0.7284 (t70) outliers start: 70 outliers final: 31 residues processed: 413 average time/residue: 0.6348 time to fit residues: 303.3208 Evaluate side-chains 376 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 344 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 28 THR 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 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 N residue 1 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain J residue 28 THR 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 375 SER Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain R residue 33 LEU 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 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 159 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 295 optimal weight: 0.9980 chunk 140 optimal weight: 0.0870 chunk 157 optimal weight: 2.9990 overall best weight: 1.1360 ------------------------------------------------------------------------------- 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** G 100BGLN A 114 GLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN ** C 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.182736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.142501 restraints weight = 25146.907| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.93 r_work: 0.3357 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25650 Z= 0.188 Angle : 0.711 13.877 34929 Z= 0.347 Chirality : 0.047 0.260 3981 Planarity : 0.004 0.038 4365 Dihedral : 8.628 73.393 4601 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.78 % Allowed : 17.31 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.14), residues: 3051 helix: -0.24 (0.23), residues: 474 sheet: -0.32 (0.15), residues: 1026 loop : -0.36 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 192 TYR 0.027 0.002 TYR F 638 PHE 0.017 0.002 PHE E 383 TRP 0.023 0.002 TRP E 112 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00430 (25545) covalent geometry : angle 0.67725 (34659) SS BOND : bond 0.00334 ( 45) SS BOND : angle 1.95894 ( 90) hydrogen bonds : bond 0.04700 ( 888) hydrogen bonds : angle 5.45657 ( 2547) link_ALPHA1-3 : bond 0.00909 ( 3) link_ALPHA1-3 : angle 1.63330 ( 9) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 2.35509 ( 54) link_NAG-ASN : bond 0.00552 ( 39) link_NAG-ASN : angle 3.06560 ( 117) *********************** 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 438 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 364 time to evaluate : 0.712 Fit side-chains REVERT: G 46 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: A 82 GLN cc_start: 0.8391 (mm-40) cc_final: 0.8109 (mp10) REVERT: A 192 ARG cc_start: 0.7627 (ttp80) cc_final: 0.7422 (ttp-110) REVERT: A 347 LYS cc_start: 0.8242 (ttpp) cc_final: 0.7723 (pttp) REVERT: A 440 GLN cc_start: 0.8046 (mt0) cc_final: 0.7696 (mp10) REVERT: B 535 MET cc_start: 0.8935 (mtp) cc_final: 0.8505 (mtm) REVERT: K 80 MET cc_start: 0.9102 (tmm) cc_final: 0.8872 (tmt) REVERT: J 18 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7201 (tt) REVERT: J 46 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: C 82 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7894 (mp10) REVERT: C 268 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7985 (mt-10) REVERT: C 271 MET cc_start: 0.8964 (mmm) cc_final: 0.8639 (mmp) REVERT: C 347 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7863 (pttp) REVERT: C 412 ASP cc_start: 0.7277 (t0) cc_final: 0.6687 (t0) REVERT: D 538 THR cc_start: 0.8889 (m) cc_final: 0.8642 (p) REVERT: D 633 LYS cc_start: 0.8111 (mttt) cc_final: 0.7500 (mtpt) REVERT: E 82 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7876 (mp10) REVERT: E 97 LYS cc_start: 0.9003 (mttm) cc_final: 0.8718 (mttt) REVERT: E 150 MET cc_start: 0.6279 (tpt) cc_final: 0.6053 (tpt) REVERT: E 269 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: E 347 LYS cc_start: 0.8431 (ttpp) cc_final: 0.7922 (pttp) REVERT: F 633 LYS cc_start: 0.7848 (mttt) cc_final: 0.7160 (mtmt) REVERT: F 659 ASP cc_start: 0.8590 (t0) cc_final: 0.7850 (t70) outliers start: 74 outliers final: 42 residues processed: 409 average time/residue: 0.6980 time to fit residues: 327.3139 Evaluate side-chains 388 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 342 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain J residue 18 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 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 D residue 546 SER 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 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 269 GLU 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 F residue 639 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 34 optimal weight: 0.5980 chunk 120 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 298 optimal weight: 0.5980 chunk 155 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN L 89 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.181948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140894 restraints weight = 25062.896| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.01 r_work: 0.3312 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 25650 Z= 0.190 Angle : 0.695 11.445 34929 Z= 0.339 Chirality : 0.046 0.263 3981 Planarity : 0.004 0.042 4365 Dihedral : 7.900 74.591 4601 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.93 % Allowed : 18.70 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.14), residues: 3051 helix: 0.06 (0.24), residues: 456 sheet: -0.34 (0.16), residues: 978 loop : -0.37 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 192 TYR 0.015 0.002 TYR I 96 PHE 0.018 0.002 PHE A 383 TRP 0.021 0.002 TRP E 112 HIS 0.004 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00439 (25545) covalent geometry : angle 0.65791 (34659) SS BOND : bond 0.00352 ( 45) SS BOND : angle 1.96819 ( 90) hydrogen bonds : bond 0.04487 ( 888) hydrogen bonds : angle 5.37915 ( 2547) link_ALPHA1-3 : bond 0.00808 ( 3) link_ALPHA1-3 : angle 1.65910 ( 9) link_BETA1-4 : bond 0.00514 ( 18) link_BETA1-4 : angle 2.46033 ( 54) link_NAG-ASN : bond 0.00510 ( 39) link_NAG-ASN : angle 3.17638 ( 117) *********************** 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 434 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 356 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: G 46 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7773 (tm-30) REVERT: A 82 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8136 (mp10) REVERT: A 192 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7251 (ttp-170) REVERT: A 347 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7781 (pttp) REVERT: A 440 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: B 535 MET cc_start: 0.8958 (mtp) cc_final: 0.8530 (mtm) REVERT: K 80 MET cc_start: 0.9158 (tmm) cc_final: 0.8849 (tmt) REVERT: M 42 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7919 (ptmt) REVERT: C 49 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8850 (mt-10) REVERT: C 82 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8039 (mp10) REVERT: C 268 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 271 MET cc_start: 0.8994 (mmm) cc_final: 0.8635 (mmp) REVERT: C 278 ARG cc_start: 0.8889 (mmm160) cc_final: 0.8558 (mmm160) REVERT: C 347 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7918 (pttp) REVERT: D 538 THR cc_start: 0.8998 (m) cc_final: 0.8709 (p) REVERT: D 633 LYS cc_start: 0.8134 (mttt) cc_final: 0.7514 (mtpt) REVERT: D 648 GLU cc_start: 0.4189 (OUTLIER) cc_final: 0.3973 (pt0) REVERT: P 94 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8117 (tmt170) REVERT: O 18 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7143 (tt) REVERT: O 46 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8509 (tt0) REVERT: E 82 GLN cc_start: 0.8292 (mm-40) cc_final: 0.7902 (mp10) REVERT: E 97 LYS cc_start: 0.8990 (mttm) cc_final: 0.8689 (mtmt) REVERT: E 269 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7723 (mt-10) REVERT: E 347 LYS cc_start: 0.8453 (ttpp) cc_final: 0.7953 (pttp) REVERT: F 633 LYS cc_start: 0.7902 (mttt) cc_final: 0.7192 (mtmt) REVERT: F 659 ASP cc_start: 0.8716 (t0) cc_final: 0.7967 (t70) outliers start: 78 outliers final: 49 residues processed: 402 average time/residue: 0.6936 time to fit residues: 319.8645 Evaluate side-chains 393 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 338 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 17 SER Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 20 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 I residue 34 SER 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 375 SER Chi-restraints excluded: chain A residue 426 MET 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 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 82 MET 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 156 ASN Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 290 THR 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 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 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 Q residue 24 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 74 CYS 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 446 VAL 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 196 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 259 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 288 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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 P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 616 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.181842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.141793 restraints weight = 24965.088| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.04 r_work: 0.3342 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25650 Z= 0.178 Angle : 0.661 11.341 34929 Z= 0.324 Chirality : 0.045 0.365 3981 Planarity : 0.004 0.035 4365 Dihedral : 7.325 73.849 4601 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.63 % Allowed : 19.26 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.15), residues: 3051 helix: 0.17 (0.24), residues: 456 sheet: -0.27 (0.15), residues: 1035 loop : -0.34 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 503 TYR 0.015 0.001 TYR I 96 PHE 0.016 0.001 PHE C 383 TRP 0.022 0.002 TRP E 112 HIS 0.004 0.001 HIS O 82A Details of bonding type rmsd covalent geometry : bond 0.00410 (25545) covalent geometry : angle 0.62236 (34659) SS BOND : bond 0.00339 ( 45) SS BOND : angle 1.72830 ( 90) hydrogen bonds : bond 0.04297 ( 888) hydrogen bonds : angle 5.27905 ( 2547) link_ALPHA1-3 : bond 0.00758 ( 3) link_ALPHA1-3 : angle 1.61872 ( 9) link_BETA1-4 : bond 0.00570 ( 18) link_BETA1-4 : angle 2.37845 ( 54) link_NAG-ASN : bond 0.00441 ( 39) link_NAG-ASN : angle 3.22826 ( 117) *********************** 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 423 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 0.986 Fit side-chains REVERT: G 46 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: I 95 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7425 (p) REVERT: A 82 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8085 (mp10) REVERT: A 192 ARG cc_start: 0.7777 (ttp80) cc_final: 0.7257 (ttp-170) REVERT: A 347 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7744 (pttp) REVERT: A 440 GLN cc_start: 0.8081 (mt0) cc_final: 0.7738 (mp10) REVERT: B 535 MET cc_start: 0.8932 (mtp) cc_final: 0.8508 (mtm) REVERT: K 80 MET cc_start: 0.9150 (tmm) cc_final: 0.8865 (tmt) REVERT: M 42 LYS cc_start: 0.8200 (mtmm) cc_final: 0.7882 (ptmt) REVERT: C 49 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8712 (mt-10) REVERT: C 82 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8015 (mp10) REVERT: C 268 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 271 MET cc_start: 0.8959 (mmm) cc_final: 0.8605 (mmp) REVERT: C 278 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8549 (mmm160) REVERT: C 347 LYS cc_start: 0.8359 (ttpp) cc_final: 0.7856 (pttp) REVERT: C 372 THR cc_start: 0.8307 (p) cc_final: 0.8100 (p) REVERT: D 538 THR cc_start: 0.8979 (m) cc_final: 0.8666 (p) REVERT: D 659 ASP cc_start: 0.8609 (t0) cc_final: 0.8012 (t70) REVERT: P 94 ARG cc_start: 0.8341 (ttp-170) cc_final: 0.8100 (tmt170) REVERT: R 61 ARG cc_start: 0.6595 (ptt-90) cc_final: 0.6369 (ptt-90) REVERT: O 18 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7093 (tt) REVERT: E 82 GLN cc_start: 0.8283 (mm-40) cc_final: 0.7884 (mp10) REVERT: E 97 LYS cc_start: 0.9010 (mttm) cc_final: 0.8712 (mttt) REVERT: E 347 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7934 (pttp) REVERT: F 633 LYS cc_start: 0.7810 (mttt) cc_final: 0.7096 (mtmt) REVERT: F 659 ASP cc_start: 0.8655 (t0) cc_final: 0.7994 (t70) outliers start: 70 outliers final: 43 residues processed: 399 average time/residue: 0.7189 time to fit residues: 327.9743 Evaluate side-chains 386 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.977 ------------------------------------------------------------------------------- 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 I residue 34 SER 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 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 33 LEU 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 82 MET 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 269 GLU Chi-restraints excluded: chain C residue 290 THR 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 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 Q residue 24 THR Chi-restraints excluded: chain E residue 67 ASN 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 F residue 639 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 136 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 270 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 206 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** G 100BGLN ** A 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN ** F 650 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 = 0.3978 r_free = 0.3978 target = 0.182751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142917 restraints weight = 25055.241| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.98 r_work: 0.3334 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2378 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= 0.143 Angle : 0.628 11.604 34929 Z= 0.307 Chirality : 0.045 0.474 3981 Planarity : 0.004 0.035 4365 Dihedral : 7.049 72.576 4599 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.56 % Allowed : 19.64 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 3051 helix: 0.32 (0.25), residues: 456 sheet: -0.21 (0.16), residues: 999 loop : -0.28 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.013 0.001 TYR I 96 PHE 0.014 0.001 PHE A 383 TRP 0.021 0.002 TRP C 112 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00323 (25545) covalent geometry : angle 0.58454 (34659) SS BOND : bond 0.00278 ( 45) SS BOND : angle 1.57778 ( 90) hydrogen bonds : bond 0.03982 ( 888) hydrogen bonds : angle 5.18042 ( 2547) link_ALPHA1-3 : bond 0.00772 ( 3) link_ALPHA1-3 : angle 1.55587 ( 9) link_BETA1-4 : bond 0.00506 ( 18) link_BETA1-4 : angle 2.28138 ( 54) link_NAG-ASN : bond 0.00327 ( 39) link_NAG-ASN : angle 3.48600 ( 117) *********************** 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 418 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 350 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: H 87 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7830 (p) REVERT: G 46 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: A 82 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8087 (mp10) REVERT: A 192 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7375 (ttp-170) REVERT: A 347 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7766 (pttp) REVERT: A 440 GLN cc_start: 0.8053 (mt0) cc_final: 0.7732 (mp10) REVERT: B 535 MET cc_start: 0.8932 (mtp) cc_final: 0.8513 (mtm) REVERT: K 80 MET cc_start: 0.9176 (tmm) cc_final: 0.8878 (tmt) REVERT: M 42 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7855 (ptmt) REVERT: C 49 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8674 (mt-10) REVERT: C 82 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7998 (mp10) REVERT: C 268 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 271 MET cc_start: 0.8959 (mmm) cc_final: 0.8601 (mmp) REVERT: C 278 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8573 (mmm160) REVERT: C 347 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7899 (pttp) REVERT: C 372 THR cc_start: 0.8301 (p) cc_final: 0.8093 (p) REVERT: D 538 THR cc_start: 0.8927 (m) cc_final: 0.8655 (p) REVERT: P 94 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.8120 (tmt170) REVERT: R 61 ARG cc_start: 0.6597 (ptt-90) cc_final: 0.6362 (ptt-90) REVERT: Q 95 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7664 (p) REVERT: E 82 GLN cc_start: 0.8289 (mm-40) cc_final: 0.7903 (mp10) REVERT: E 97 LYS cc_start: 0.9024 (mttm) cc_final: 0.8733 (mttt) REVERT: E 347 LYS cc_start: 0.8443 (ttpp) cc_final: 0.7949 (pttp) REVERT: F 633 LYS cc_start: 0.7802 (mttt) cc_final: 0.7113 (mtmt) REVERT: F 659 ASP cc_start: 0.8664 (t0) cc_final: 0.7919 (t70) outliers start: 68 outliers final: 45 residues processed: 396 average time/residue: 0.7096 time to fit residues: 321.9042 Evaluate side-chains 389 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 341 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 87 THR 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 I residue 24 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain N residue 33 LEU 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 82 MET 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 156 ASN 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 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 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 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 E residue 430 ILE 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 137 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 301 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 274 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100BGLN C 377 ASN D 650 GLN P 64 GLN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3978 r_free = 0.3978 target = 0.182863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.142750 restraints weight = 24949.986| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.87 r_work: 0.3322 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25650 Z= 0.144 Angle : 0.623 12.471 34929 Z= 0.304 Chirality : 0.045 0.571 3981 Planarity : 0.004 0.034 4365 Dihedral : 6.697 71.573 4599 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.82 % Allowed : 19.68 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.15), residues: 3051 helix: 0.16 (0.24), residues: 474 sheet: -0.19 (0.16), residues: 999 loop : -0.19 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.015 0.001 TYR I 96 PHE 0.013 0.001 PHE C 383 TRP 0.018 0.002 TRP C 112 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00328 (25545) covalent geometry : angle 0.57836 (34659) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.40498 ( 90) hydrogen bonds : bond 0.03931 ( 888) hydrogen bonds : angle 5.12884 ( 2547) link_ALPHA1-3 : bond 0.00709 ( 3) link_ALPHA1-3 : angle 1.54041 ( 9) link_BETA1-4 : bond 0.00511 ( 18) link_BETA1-4 : angle 2.25337 ( 54) link_NAG-ASN : bond 0.00315 ( 39) link_NAG-ASN : angle 3.57731 ( 117) *********************** 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 433 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 358 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: G 46 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7701 (tm-30) REVERT: G 82 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (mtm) REVERT: I 95 THR cc_start: 0.7929 (OUTLIER) cc_final: 0.7349 (p) REVERT: A 82 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7961 (mp10) REVERT: A 192 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7225 (ttp-170) REVERT: A 347 LYS cc_start: 0.8171 (ttpp) cc_final: 0.7642 (pttp) REVERT: A 426 MET cc_start: 0.8286 (mmm) cc_final: 0.7991 (mtt) REVERT: A 440 GLN cc_start: 0.7977 (mt0) cc_final: 0.7617 (mp10) REVERT: A 444 ARG cc_start: 0.8007 (tmt170) cc_final: 0.7584 (ttt180) REVERT: B 535 MET cc_start: 0.8828 (mtp) cc_final: 0.8413 (mtm) REVERT: K 10 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: K 80 MET cc_start: 0.9116 (tmm) cc_final: 0.8791 (tmt) REVERT: M 42 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7920 (ptmt) REVERT: C 49 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8452 (mt-10) REVERT: C 82 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7879 (mp10) REVERT: C 268 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7942 (mt-10) REVERT: C 271 MET cc_start: 0.8855 (mmm) cc_final: 0.8547 (mmp) REVERT: C 278 ARG cc_start: 0.8795 (mmm160) cc_final: 0.8464 (mmm160) REVERT: C 321 ASP cc_start: 0.7198 (t0) cc_final: 0.6930 (t0) REVERT: C 347 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7796 (pttp) REVERT: C 372 THR cc_start: 0.8232 (p) cc_final: 0.8027 (p) REVERT: D 538 THR cc_start: 0.8875 (m) cc_final: 0.8513 (p) REVERT: D 659 ASP cc_start: 0.8398 (t0) cc_final: 0.7915 (t0) REVERT: P 10 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: P 66 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7762 (ttp80) REVERT: P 94 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.8074 (tmt170) REVERT: R 61 ARG cc_start: 0.6475 (ptt-90) cc_final: 0.6259 (ptt-90) REVERT: O 18 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7182 (tt) REVERT: Q 95 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7576 (p) REVERT: E 82 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7829 (mp10) REVERT: E 97 LYS cc_start: 0.8956 (mttm) cc_final: 0.8650 (mttt) REVERT: F 652 GLN cc_start: 0.8024 (mt0) cc_final: 0.7810 (pt0) REVERT: F 659 ASP cc_start: 0.8477 (t0) cc_final: 0.7912 (t70) outliers start: 75 outliers final: 49 residues processed: 409 average time/residue: 0.6962 time to fit residues: 327.5221 Evaluate side-chains 398 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 342 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 23 ARG Chi-restraints excluded: chain G residue 46 GLU 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 I residue 34 SER 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 290 THR 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 62 SER Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 82 MET 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 156 ASN 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 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 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 11 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 87 THR Chi-restraints excluded: chain O residue 110 THR 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 269 GLU Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 430 ILE 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 169 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 268 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 292 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** ** 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 377 ASN F 650 GLN F 653 GLN F 658 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.182465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.140447 restraints weight = 25002.220| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.47 r_work: 0.3336 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25650 Z= 0.247 Angle : 0.727 17.666 34929 Z= 0.356 Chirality : 0.048 0.438 3981 Planarity : 0.005 0.036 4365 Dihedral : 6.717 74.141 4599 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.20 % Allowed : 19.75 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.15), residues: 3051 helix: 0.09 (0.24), residues: 459 sheet: -0.28 (0.16), residues: 993 loop : -0.28 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 503 TYR 0.016 0.002 TYR I 96 PHE 0.019 0.002 PHE A 383 TRP 0.021 0.002 TRP E 112 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00578 (25545) covalent geometry : angle 0.67836 (34659) SS BOND : bond 0.00349 ( 45) SS BOND : angle 1.95490 ( 90) hydrogen bonds : bond 0.04733 ( 888) hydrogen bonds : angle 5.39129 ( 2547) link_ALPHA1-3 : bond 0.00540 ( 3) link_ALPHA1-3 : angle 1.70940 ( 9) link_BETA1-4 : bond 0.00517 ( 18) link_BETA1-4 : angle 2.36862 ( 54) link_NAG-ASN : bond 0.00576 ( 39) link_NAG-ASN : angle 3.94635 ( 117) *********************** 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 430 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 345 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 72 ASP cc_start: 0.8135 (t70) cc_final: 0.7873 (t0) REVERT: H 82 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: L 96 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: G 46 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7738 (tm-30) REVERT: I 95 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 82 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8087 (mp10) REVERT: A 192 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7570 (ttp-170) REVERT: A 347 LYS cc_start: 0.8426 (ttpp) cc_final: 0.7949 (pttp) REVERT: A 440 GLN cc_start: 0.8092 (mt0) cc_final: 0.7767 (mp10) REVERT: B 535 MET cc_start: 0.8893 (mtp) cc_final: 0.8492 (mtm) REVERT: K 10 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7390 (mt-10) REVERT: N 61 ARG cc_start: 0.6776 (ptt-90) cc_final: 0.6462 (ptt-90) REVERT: M 42 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7959 (ptmt) REVERT: C 49 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8609 (mt-10) REVERT: C 82 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8079 (mp10) REVERT: C 268 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8078 (mt-10) REVERT: C 271 MET cc_start: 0.8913 (mmm) cc_final: 0.8552 (mmp) REVERT: C 278 ARG cc_start: 0.8917 (mmm160) cc_final: 0.8600 (mmm160) REVERT: C 347 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8022 (pttp) REVERT: D 659 ASP cc_start: 0.8616 (t0) cc_final: 0.8126 (t70) REVERT: P 10 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7264 (mt-10) REVERT: P 66 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7942 (ttp80) REVERT: P 94 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.7917 (ttt-90) REVERT: R 61 ARG cc_start: 0.6647 (ptt-90) cc_final: 0.6431 (ptt-90) REVERT: Q 95 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7644 (p) REVERT: E 82 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7996 (mp10) REVERT: E 97 LYS cc_start: 0.9039 (mttm) cc_final: 0.8767 (mttt) REVERT: F 633 LYS cc_start: 0.7844 (mttt) cc_final: 0.7211 (mtmt) REVERT: F 659 ASP cc_start: 0.8692 (t0) cc_final: 0.8162 (t70) outliers start: 85 outliers final: 56 residues processed: 400 average time/residue: 0.7175 time to fit residues: 329.8875 Evaluate side-chains 401 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 339 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 L residue 96 GLU 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 I residue 24 THR Chi-restraints excluded: chain I residue 34 SER 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 290 THR Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 637 ASN 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 62 SER Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 82 MET 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 54 CYS 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 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 105 ARG Chi-restraints excluded: chain R residue 1 VAL Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain O residue 11 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 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 45 LYS Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 74 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 219 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 134 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 201 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 0.0670 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 ** 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 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.183052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.143174 restraints weight = 25161.796| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.04 r_work: 0.3361 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25650 Z= 0.126 Angle : 0.621 13.912 34929 Z= 0.303 Chirality : 0.045 0.383 3981 Planarity : 0.004 0.036 4365 Dihedral : 6.349 71.271 4599 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.60 % Allowed : 20.62 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.15), residues: 3051 helix: 0.21 (0.25), residues: 471 sheet: -0.24 (0.16), residues: 1032 loop : -0.13 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 542 TYR 0.012 0.001 TYR M 96 PHE 0.012 0.001 PHE E 383 TRP 0.019 0.001 TRP C 112 HIS 0.004 0.001 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00281 (25545) covalent geometry : angle 0.56725 (34659) SS BOND : bond 0.00229 ( 45) SS BOND : angle 1.38014 ( 90) hydrogen bonds : bond 0.03772 ( 888) hydrogen bonds : angle 5.17053 ( 2547) link_ALPHA1-3 : bond 0.00650 ( 3) link_ALPHA1-3 : angle 1.48108 ( 9) link_BETA1-4 : bond 0.00601 ( 18) link_BETA1-4 : angle 2.29760 ( 54) link_NAG-ASN : bond 0.00372 ( 39) link_NAG-ASN : angle 3.97052 ( 117) *********************** 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 416 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 347 time to evaluate : 1.017 Fit side-chains REVERT: H 10 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: H 82 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7536 (mtm-85) REVERT: G 46 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: I 42 LYS cc_start: 0.8269 (mtmm) cc_final: 0.8041 (ptpt) REVERT: I 95 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7405 (p) REVERT: A 82 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8025 (mp10) REVERT: A 192 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7445 (ttp-170) REVERT: A 347 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7759 (pttp) REVERT: A 426 MET cc_start: 0.8344 (mmm) cc_final: 0.8082 (mtt) REVERT: A 440 GLN cc_start: 0.8025 (mt0) cc_final: 0.7661 (mp10) REVERT: A 444 ARG cc_start: 0.7959 (tmt170) cc_final: 0.7585 (ttt180) REVERT: B 535 MET cc_start: 0.8923 (mtp) cc_final: 0.8512 (mtm) REVERT: K 10 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: K 80 MET cc_start: 0.9164 (tmm) cc_final: 0.8827 (tmt) REVERT: K 96 MET cc_start: 0.8662 (ptm) cc_final: 0.8403 (ptm) REVERT: J 46 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7599 (tm-30) REVERT: C 49 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 82 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7972 (mp10) REVERT: C 268 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8080 (mt-10) REVERT: C 271 MET cc_start: 0.8897 (mmm) cc_final: 0.8553 (mmp) REVERT: C 278 ARG cc_start: 0.8872 (mmm160) cc_final: 0.8545 (mmm160) REVERT: C 347 LYS cc_start: 0.8357 (ttpp) cc_final: 0.7859 (pttp) REVERT: C 372 THR cc_start: 0.8259 (p) cc_final: 0.8051 (p) REVERT: P 10 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: P 66 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7701 (ttp80) REVERT: P 94 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.7908 (ttt-90) REVERT: P 98 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7687 (p0) REVERT: R 61 ARG cc_start: 0.6464 (ptt-90) cc_final: 0.6241 (ptt-90) REVERT: Q 95 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7540 (p) REVERT: E 82 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7940 (mp10) REVERT: E 97 LYS cc_start: 0.9003 (mttm) cc_final: 0.8709 (mttt) REVERT: E 347 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7906 (pttp) REVERT: F 659 ASP cc_start: 0.8588 (t0) cc_final: 0.7891 (t70) outliers start: 69 outliers final: 43 residues processed: 390 average time/residue: 0.6212 time to fit residues: 279.5795 Evaluate side-chains 388 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 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 I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL 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 10 GLU 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 54 CYS 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 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 33 LEU Chi-restraints excluded: chain O residue 18 LEU 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 26 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 290 THR 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: 2.9990 chunk 148 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 161 optimal weight: 4.9990 chunk 282 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** ** 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 67 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 ASN F 658 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.182905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.142161 restraints weight = 25086.771| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.03 r_work: 0.3336 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25650 Z= 0.144 Angle : 0.653 19.579 34929 Z= 0.318 Chirality : 0.047 0.805 3981 Planarity : 0.004 0.034 4365 Dihedral : 6.473 70.166 4599 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.96 % Allowed : 21.44 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.15), residues: 3051 helix: 0.31 (0.25), residues: 450 sheet: -0.15 (0.16), residues: 996 loop : -0.08 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.012 0.001 TYR I 96 PHE 0.014 0.001 PHE E 383 TRP 0.020 0.002 TRP C 112 HIS 0.006 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00324 (25545) covalent geometry : angle 0.59311 (34659) SS BOND : bond 0.00241 ( 45) SS BOND : angle 1.38877 ( 90) hydrogen bonds : bond 0.03907 ( 888) hydrogen bonds : angle 5.17178 ( 2547) link_ALPHA1-3 : bond 0.00608 ( 3) link_ALPHA1-3 : angle 1.52519 ( 9) link_BETA1-4 : bond 0.00579 ( 18) link_BETA1-4 : angle 2.22612 ( 54) link_NAG-ASN : bond 0.00847 ( 39) link_NAG-ASN : angle 4.36573 ( 117) ********************** 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 390 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 338 time to evaluate : 0.975 Fit side-chains REVERT: H 10 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7478 (mt-10) REVERT: H 82 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7537 (mtm-85) REVERT: G 46 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7895 (tm-30) REVERT: I 42 LYS cc_start: 0.8262 (mtmm) cc_final: 0.8011 (ptpt) REVERT: I 95 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7424 (p) REVERT: A 82 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8026 (mp10) REVERT: A 192 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7403 (ttp-170) REVERT: A 347 LYS cc_start: 0.8297 (ttpp) cc_final: 0.7775 (pttp) REVERT: A 440 GLN cc_start: 0.8027 (mt0) cc_final: 0.7650 (mp10) REVERT: A 444 ARG cc_start: 0.7996 (tmt170) cc_final: 0.7643 (tpt170) REVERT: B 535 MET cc_start: 0.8930 (mtp) cc_final: 0.8508 (mtm) REVERT: K 10 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7428 (mt-10) REVERT: K 66 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7845 (ttt-90) REVERT: K 80 MET cc_start: 0.9153 (tmm) cc_final: 0.8831 (tmt) REVERT: N 61 ARG cc_start: 0.6633 (ptt-90) cc_final: 0.6248 (ptt-90) REVERT: J 46 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: C 49 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8721 (mt-10) REVERT: C 82 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7939 (mp10) REVERT: C 268 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8059 (mt-10) REVERT: C 271 MET cc_start: 0.8913 (mmm) cc_final: 0.8562 (mmp) REVERT: C 278 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8575 (mmm160) REVERT: C 347 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7941 (pttp) REVERT: C 372 THR cc_start: 0.8301 (p) cc_final: 0.8096 (p) REVERT: D 659 ASP cc_start: 0.8586 (t0) cc_final: 0.7865 (t0) REVERT: P 10 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: P 66 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7694 (ttp80) REVERT: P 94 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.7904 (ttt-90) REVERT: P 98 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7761 (p0) REVERT: R 61 ARG cc_start: 0.6449 (ptt-90) cc_final: 0.6202 (ptt-90) REVERT: O 18 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7017 (tt) REVERT: Q 95 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.7578 (p) REVERT: E 82 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7920 (mp10) REVERT: E 97 LYS cc_start: 0.9065 (mttm) cc_final: 0.8793 (mttt) REVERT: F 633 LYS cc_start: 0.7836 (mttt) cc_final: 0.7124 (mtmt) REVERT: F 647 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7740 (tm-30) REVERT: F 652 GLN cc_start: 0.8393 (mt0) cc_final: 0.8124 (pt0) REVERT: F 659 ASP cc_start: 0.8654 (t0) cc_final: 0.7895 (t70) outliers start: 52 outliers final: 37 residues processed: 372 average time/residue: 0.6709 time to fit residues: 286.1633 Evaluate side-chains 377 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 331 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 25 SER 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 I residue 24 THR Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 182 VAL 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 10 GLU Chi-restraints excluded: chain N residue 33 LEU 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 54 CYS 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 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 R residue 33 LEU Chi-restraints excluded: chain O residue 18 LEU 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 26 THR Chi-restraints excluded: chain Q residue 95 THR Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 74 CYS Chi-restraints excluded: chain E residue 290 THR 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 133 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 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** ** 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 ** O 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN F 658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.182539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.142593 restraints weight = 24991.662| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.99 r_work: 0.3330 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25650 Z= 0.152 Angle : 0.648 15.780 34929 Z= 0.317 Chirality : 0.048 0.640 3981 Planarity : 0.004 0.038 4365 Dihedral : 6.286 68.019 4599 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.03 % Allowed : 21.41 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.15), residues: 3051 helix: 0.29 (0.25), residues: 465 sheet: -0.14 (0.16), residues: 996 loop : -0.12 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 542 TYR 0.012 0.001 TYR M 96 PHE 0.014 0.001 PHE A 383 TRP 0.024 0.002 TRP A 112 HIS 0.006 0.001 HIS O 82A Details of bonding type rmsd covalent geometry : bond 0.00344 (25545) covalent geometry : angle 0.59381 (34659) SS BOND : bond 0.00243 ( 45) SS BOND : angle 1.39327 ( 90) hydrogen bonds : bond 0.04006 ( 888) hydrogen bonds : angle 5.20251 ( 2547) link_ALPHA1-3 : bond 0.00533 ( 3) link_ALPHA1-3 : angle 1.51373 ( 9) link_BETA1-4 : bond 0.00559 ( 18) link_BETA1-4 : angle 2.15652 ( 54) link_NAG-ASN : bond 0.00568 ( 39) link_NAG-ASN : angle 4.13258 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10069.26 seconds wall clock time: 172 minutes 8.06 seconds (10328.06 seconds total)