Starting phenix.real_space_refine on Fri May 23 02:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlk_14783/05_2025/7zlk_14783.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 141 5.16 5 C 14758 2.51 5 N 3941 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23518 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 954 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "C" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "E" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 982 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "D" Number of atoms: 3460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3460 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1058 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "M" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "N" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "P" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "Q" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "R" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 856 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain: "T" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 814 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" 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: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Y" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "c" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "d" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "e" 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: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 13.34, per 1000 atoms: 0.57 Number of scatterers: 23518 At special positions: 0 Unit cell: (151.8, 151.8, 170.2, 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 141 16.00 O 4678 8.00 N 3941 7.00 C 14758 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.12 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.19 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.07 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.02 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.04 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 21 " - pdb=" SG CYS N 86 " distance=2.02 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.02 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.02 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 92 " distance=2.03 Simple disulfide: pdb=" SG CYS T 21 " - pdb=" SG CYS T 86 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN d 4 " - " MAN d 5 " ALPHA1-3 " BMA I 3 " - " MAN I 4 " " BMA J 3 " - " MAN J 7 " " MAN J 4 " - " MAN J 5 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 7 " " MAN X 4 " - " MAN X 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA c 3 " - " MAN c 7 " " MAN c 4 " - " MAN c 5 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 6 " " BMA K 3 " - " MAN K 4 " " BMA U 3 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 4 " " MAN X 4 " - " MAN X 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 5 " " BMA b 3 " - " MAN b 5 " " BMA c 3 " - " MAN c 4 " " MAN c 4 " - " MAN c 6 " " BMA d 3 " - " MAN d 6 " " MAN d 6 " - " MAN d 8 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 241 " " NAG A 604 " - " ASN A 188 " " NAG A 605 " - " ASN A 362 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 156 " " NAG C 603 " - " ASN C 241 " " NAG C 604 " - " ASN C 188 " " NAG C 605 " - " ASN C 362 " " NAG C 606 " - " ASN C 386 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 88 " " NAG D 601 " - " ASN D 156 " " NAG D 602 " - " ASN D 234 " " NAG D 603 " - " ASN D 241 " " NAG D 604 " - " ASN D 289 " " NAG D 605 " - " ASN D 189 " " NAG D 606 " - " ASN D 362 " " NAG D 607 " - " ASN D 386 " " NAG D 608 " - " ASN D 88 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 295 " " NAG K 1 " - " ASN A 301 " " NAG U 1 " - " ASN A 332 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 295 " " NAG Y 1 " - " ASN C 301 " " NAG Z 1 " - " ASN C 332 " " NAG a 1 " - " ASN C 448 " " NAG b 1 " - " ASN D 262 " " NAG c 1 " - " ASN D 295 " " NAG d 1 " - " ASN D 332 " " NAG e 1 " - " ASN D 448 " " NAG f 1 " - " ASN D 301 " Time building additional restraints: 6.86 Conformation dependent library (CDL) restraints added in 2.7 seconds 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 19.5% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.044A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 338 through 350 removed outlier: 4.053A pdb=" N ARG A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 540 through 545 removed outlier: 3.995A pdb=" N GLN B 543 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU B 544 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 545 " --> pdb=" O ARG B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 540 through 545' Processing helix chain 'B' and resid 548 through 558 Processing helix chain 'B' and resid 569 through 596 removed outlier: 5.482A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 631 through 649 removed outlier: 4.014A pdb=" N ASN B 637 " --> pdb=" O ARG B 633 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN B 644 " --> pdb=" O GLY B 640 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 647 " --> pdb=" O TYR B 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.566A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 476 through 484 removed outlier: 5.293A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 535 Processing helix chain 'E' and resid 536 through 545 removed outlier: 3.614A pdb=" N GLN E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 625 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 652 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.611A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.889A pdb=" N LYS D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 481 removed outlier: 3.516A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 543 through 550 removed outlier: 3.879A pdb=" N VAL F 549 " --> pdb=" O LEU F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 556 Processing helix chain 'F' and resid 572 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 652 through 662 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.599A pdb=" N HIS M 32 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 65 removed outlier: 5.648A pdb=" N SER M 65 " --> pdb=" O SER M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 77 through 81 Processing helix chain 'O' and resid 41 through 43 No H-bonds generated for 'chain 'O' and resid 41 through 43' Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 Processing helix chain 'Q' and resid 41 through 43 No H-bonds generated for 'chain 'Q' and resid 41 through 43' Processing helix chain 'Q' and resid 61 through 64 Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.503A pdb=" N HIS S 32 " --> pdb=" O ILE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 65 removed outlier: 5.733A pdb=" N SER S 65 " --> pdb=" O SER S 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 87 Processing helix chain 'T' and resid 77 through 81 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.732A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.298A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.917A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.647A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.860A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.694A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.708A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.461A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.170A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 304 through 310 removed outlier: 6.929A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.760A pdb=" N ARG C 66 " --> pdb=" O SER C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AB3, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AB4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.350A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.876A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 298 current: chain 'C' and resid 358 through 361 Processing sheet with id=AB6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.831A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 11.089A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.913A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 12.076A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 414 through 416 Processing sheet with id=AB7, first strand: chain 'C' and resid 301 through 310 removed outlier: 6.724A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 309 " --> pdb=" O ARG C 315 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 376 through 378 removed outlier: 4.251A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.801A pdb=" N ARG D 66 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'D' and resid 171 through 177 Processing sheet with id=AC6, first strand: chain 'D' and resid 201 through 203 removed outlier: 6.714A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AC8, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 315 through 323A removed outlier: 6.906A pdb=" N ARG D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.614A pdb=" N HIS D 374 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.762A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.746A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.951A pdb=" N TYR M 33 " --> pdb=" O GLU M 95 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 11 through 12 removed outlier: 7.078A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 8 through 11 removed outlier: 6.559A pdb=" N TRP N 33 " --> pdb=" O VAL N 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 8 through 11 Processing sheet with id=AE3, first strand: chain 'N' and resid 17 through 22 Processing sheet with id=AE4, first strand: chain 'O' and resid 4 through 8 Processing sheet with id=AE5, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP O 34 " --> pdb=" O GLU O 50 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU O 50 " --> pdb=" O TRP O 34 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'O' and resid 11 through 12 Processing sheet with id=AE7, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'P' and resid 10 through 13 removed outlier: 5.948A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 4 through 8 Processing sheet with id=AF1, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.755A pdb=" N TRP Q 34 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU Q 50 " --> pdb=" O TRP Q 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 11 through 12 Processing sheet with id=AF3, first strand: chain 'R' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'R' and resid 10 through 13 removed outlier: 6.581A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 18 through 23 Processing sheet with id=AF6, first strand: chain 'S' and resid 57 through 59 removed outlier: 6.677A pdb=" N TRP S 36 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR S 50 " --> pdb=" O TRP S 34 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TRP S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TYR S 33 " --> pdb=" O GLU S 95 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 8 through 11 removed outlier: 6.606A pdb=" N TRP T 33 " --> pdb=" O VAL T 45 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 8 through 11 Processing sheet with id=AF9, first strand: chain 'T' and resid 17 through 22 889 hydrogen bonds defined for protein. 2214 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: 8.26 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 4525 1.32 - 1.46: 8381 1.46 - 1.60: 10899 1.60 - 1.75: 41 1.75 - 1.89: 181 Bond restraints: 24027 Sorted by residual: bond pdb=" N PRO S 102 " pdb=" CD PRO S 102 " ideal model delta sigma weight residual 1.473 1.615 -0.142 1.40e-02 5.10e+03 1.03e+02 bond pdb=" CB HIS D 308 " pdb=" CG HIS D 308 " ideal model delta sigma weight residual 1.497 1.395 0.102 1.40e-02 5.10e+03 5.29e+01 bond pdb=" CB LEU N 107 " pdb=" CG LEU N 107 " ideal model delta sigma weight residual 1.530 1.665 -0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" CB LEU T 107 " pdb=" CG LEU T 107 " ideal model delta sigma weight residual 1.530 1.657 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CB PHE Q 29 " pdb=" CG PHE Q 29 " ideal model delta sigma weight residual 1.502 1.365 0.137 2.30e-02 1.89e+03 3.57e+01 ... (remaining 24022 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.10: 32374 6.10 - 12.20: 285 12.20 - 18.30: 8 18.30 - 24.40: 0 24.40 - 30.51: 1 Bond angle restraints: 32668 Sorted by residual: angle pdb=" N ASP S 101 " pdb=" CA ASP S 101 " pdb=" C ASP S 101 " ideal model delta sigma weight residual 109.81 140.32 -30.51 2.21e+00 2.05e-01 1.91e+02 angle pdb=" N PHE Q 29 " pdb=" CA PHE Q 29 " pdb=" C PHE Q 29 " ideal model delta sigma weight residual 113.02 127.64 -14.62 1.20e+00 6.94e-01 1.48e+02 angle pdb=" N PHE H 29 " pdb=" CA PHE H 29 " pdb=" C PHE H 29 " ideal model delta sigma weight residual 113.02 126.23 -13.21 1.20e+00 6.94e-01 1.21e+02 angle pdb=" N THR P 92 " pdb=" CA THR P 92 " pdb=" C THR P 92 " ideal model delta sigma weight residual 111.36 122.50 -11.14 1.09e+00 8.42e-01 1.04e+02 angle pdb=" N PRO S 102 " pdb=" CA PRO S 102 " pdb=" C PRO S 102 " ideal model delta sigma weight residual 113.40 100.56 12.84 1.34e+00 5.57e-01 9.18e+01 ... (remaining 32663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 14997 21.69 - 43.38: 361 43.38 - 65.07: 100 65.07 - 86.76: 108 86.76 - 108.45: 57 Dihedral angle restraints: 15623 sinusoidal: 7453 harmonic: 8170 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 -86.00 -164.40 78.40 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -163.72 77.72 1 1.00e+01 1.00e-02 7.56e+01 dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -140.56 54.56 1 1.00e+01 1.00e-02 4.03e+01 ... (remaining 15620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3091 0.141 - 0.283: 659 0.283 - 0.424: 152 0.424 - 0.565: 42 0.565 - 0.707: 2 Chirality restraints: 3946 Sorted by residual: chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.47e+02 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 3943 not shown) Planarity restraints: 4037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " -0.314 2.00e-02 2.50e+03 2.73e-01 9.31e+02 pdb=" C7 NAG b 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.039 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " -0.196 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 608 " 0.254 2.00e-02 2.50e+03 2.10e-01 5.53e+02 pdb=" C7 NAG D 608 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG D 608 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG D 608 " -0.347 2.00e-02 2.50e+03 pdb=" O7 NAG D 608 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 603 " 0.225 2.00e-02 2.50e+03 1.92e-01 4.61e+02 pdb=" C7 NAG D 603 " -0.051 2.00e-02 2.50e+03 pdb=" C8 NAG D 603 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG D 603 " -0.315 2.00e-02 2.50e+03 pdb=" O7 NAG D 603 " 0.176 2.00e-02 2.50e+03 ... (remaining 4034 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7414 2.86 - 3.37: 21544 3.37 - 3.88: 39653 3.88 - 4.39: 45561 4.39 - 4.90: 72660 Nonbonded interactions: 186832 Sorted by model distance: nonbonded pdb=" O PHE S 100H" pdb=" NE1 TRP S 103 " model vdw 2.348 3.120 nonbonded pdb=" N ALA F 541 " pdb=" O ALA F 541 " model vdw 2.357 2.496 nonbonded pdb=" N ALA B 533 " pdb=" N SER B 534 " model vdw 2.375 2.560 nonbonded pdb=" OD1 ASP A 113 " pdb=" NZ LYS A 429 " model vdw 2.380 3.120 nonbonded pdb=" NZ LYS D 500 " pdb=" OD2 ASP N 51 " model vdw 2.394 3.120 ... (remaining 186827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 35 through 502 or resid 601 through 605)) selection = (chain 'D' and (resid 35 through 502 or resid 601 through 605)) } ncs_group { reference = (chain 'B' and (resid 523 through 558 or resid 569 through 651)) selection = (chain 'E' and resid 523 through 651) selection = (chain 'F' and resid 523 through 651) } ncs_group { reference = chain 'G' selection = chain 'V' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'f' } ncs_group { reference = (chain 'J' and (resid 1 or resid 4 through 7)) selection = (chain 'X' and (resid 1 or resid 4 through 7)) selection = (chain 'c' and (resid 1 or resid 4 through 7)) selection = (chain 'd' and (resid 2 or resid 5 through 8)) } ncs_group { reference = chain 'L' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'M' and resid 1 through 108) selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 50.940 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.155 24168 Z= 1.154 Angle : 1.889 30.506 33048 Z= 1.219 Chirality : 0.131 0.707 3946 Planarity : 0.011 0.273 4000 Dihedral : 14.463 108.451 10232 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.15), residues: 2780 helix: -0.23 (0.23), residues: 387 sheet: 0.75 (0.16), residues: 844 loop : 0.16 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.011 TRP O 47 HIS 0.009 0.002 HIS C 374 PHE 0.050 0.007 PHE M 52 TYR 0.062 0.009 TYR T 48 ARG 0.009 0.001 ARG A 469 Details of bonding type rmsd link_NAG-ASN : bond 0.07577 ( 37) link_NAG-ASN : angle 2.84058 ( 111) link_ALPHA1-6 : bond 0.05772 ( 16) link_ALPHA1-6 : angle 3.21648 ( 48) link_BETA1-4 : bond 0.07357 ( 29) link_BETA1-4 : angle 5.36914 ( 87) link_ALPHA1-2 : bond 0.08518 ( 1) link_ALPHA1-2 : angle 7.57404 ( 3) link_ALPHA1-3 : bond 0.08828 ( 15) link_ALPHA1-3 : angle 5.33909 ( 45) hydrogen bonds : bond 0.16644 ( 842) hydrogen bonds : angle 7.63685 ( 2214) SS BOND : bond 0.02853 ( 43) SS BOND : angle 3.16760 ( 86) covalent geometry : bond 0.02141 (24027) covalent geometry : angle 1.84932 (32668) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 872 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8654 (t) cc_final: 0.8396 (p) REVERT: A 78 ASP cc_start: 0.8379 (m-30) cc_final: 0.7796 (t70) REVERT: A 95 MET cc_start: 0.8766 (ptt) cc_final: 0.8552 (ppp) REVERT: A 180 ASP cc_start: 0.8380 (m-30) cc_final: 0.8164 (m-30) REVERT: A 284 ILE cc_start: 0.8443 (mt) cc_final: 0.8050 (tt) REVERT: A 368 ASP cc_start: 0.8253 (t0) cc_final: 0.7972 (t0) REVERT: A 387 THR cc_start: 0.8315 (p) cc_final: 0.8029 (t) REVERT: A 391 PHE cc_start: 0.8865 (m-80) cc_final: 0.8665 (m-10) REVERT: A 426 MET cc_start: 0.6826 (mtp) cc_final: 0.6424 (mtm) REVERT: B 523 LEU cc_start: 0.8850 (mt) cc_final: 0.8547 (mt) REVERT: B 530 MET cc_start: 0.3290 (mmp) cc_final: 0.2913 (mmp) REVERT: B 624 ASN cc_start: 0.6565 (m-40) cc_final: 0.5289 (t0) REVERT: B 631 TRP cc_start: 0.6428 (m-10) cc_final: 0.6179 (m-10) REVERT: C 42 VAL cc_start: 0.9391 (t) cc_final: 0.9185 (p) REVERT: C 68 VAL cc_start: 0.9051 (p) cc_final: 0.8726 (p) REVERT: C 103 GLN cc_start: 0.8420 (tp40) cc_final: 0.7815 (tm-30) REVERT: C 165 ILE cc_start: 0.8293 (mt) cc_final: 0.8031 (mm) REVERT: C 370 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7838 (mp0) REVERT: C 419 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7876 (mtp180) REVERT: E 530 MET cc_start: 0.8201 (mtp) cc_final: 0.7736 (mtm) REVERT: E 601 LYS cc_start: 0.8310 (mttt) cc_final: 0.7629 (mtmt) REVERT: E 618 SER cc_start: 0.8218 (m) cc_final: 0.7981 (p) REVERT: E 638 TYR cc_start: 0.8011 (m-80) cc_final: 0.7635 (m-80) REVERT: E 639 THR cc_start: 0.8432 (m) cc_final: 0.7565 (t) REVERT: E 644 ASN cc_start: 0.8449 (m-40) cc_final: 0.8181 (t0) REVERT: E 648 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8192 (mt-10) REVERT: D 92 ASN cc_start: 0.7693 (t0) cc_final: 0.7459 (t0) REVERT: D 198 THR cc_start: 0.8509 (m) cc_final: 0.8252 (p) REVERT: D 246 GLN cc_start: 0.7241 (mp10) cc_final: 0.5893 (tp40) REVERT: D 373 MET cc_start: 0.7682 (mtm) cc_final: 0.6953 (mtp) REVERT: D 434 MET cc_start: 0.8221 (ttm) cc_final: 0.7980 (ttp) REVERT: D 468 PHE cc_start: 0.7609 (m-80) cc_final: 0.6947 (m-80) REVERT: F 540 GLN cc_start: 0.8985 (tp40) cc_final: 0.8493 (tp40) REVERT: F 545 LEU cc_start: 0.9008 (tp) cc_final: 0.8498 (tt) REVERT: F 601 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8718 (mmtp) REVERT: F 623 TRP cc_start: 0.9149 (m100) cc_final: 0.8679 (m100) REVERT: H 81 LYS cc_start: 0.8180 (tttt) cc_final: 0.7919 (mmtm) REVERT: H 82 MET cc_start: 0.6850 (tpp) cc_final: 0.6322 (tpp) REVERT: H 93 VAL cc_start: 0.8808 (t) cc_final: 0.8212 (m) REVERT: H 110 LEU cc_start: 0.8435 (tp) cc_final: 0.8228 (tp) REVERT: L 27 GLN cc_start: 0.7333 (tp-100) cc_final: 0.7045 (tm-30) REVERT: L 27 LEU cc_start: 0.8126 (mt) cc_final: 0.7794 (mt) REVERT: L 60 ASP cc_start: 0.8466 (p0) cc_final: 0.8173 (p0) REVERT: L 61 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.8008 (mtm-85) REVERT: L 97 THR cc_start: 0.8924 (t) cc_final: 0.8688 (t) REVERT: M 72 ASP cc_start: 0.7924 (t0) cc_final: 0.7422 (t0) REVERT: M 86 ASP cc_start: 0.8216 (m-30) cc_final: 0.7948 (m-30) REVERT: M 91 TYR cc_start: 0.7775 (m-80) cc_final: 0.7540 (m-80) REVERT: M 100 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8372 (tt0) REVERT: N 49 ASP cc_start: 0.8065 (m-30) cc_final: 0.7794 (m-30) REVERT: N 52 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7207 (mtp-110) REVERT: N 60 PHE cc_start: 0.7893 (m-80) cc_final: 0.7245 (m-80) REVERT: N 70 THR cc_start: 0.8612 (m) cc_final: 0.8335 (t) REVERT: N 81 GLU cc_start: 0.8825 (tt0) cc_final: 0.8519 (mm-30) REVERT: N 83 ASP cc_start: 0.7982 (m-30) cc_final: 0.7405 (p0) REVERT: N 87 GLN cc_start: 0.8709 (tt0) cc_final: 0.8287 (tt0) REVERT: N 93 ARG cc_start: 0.8650 (mtt90) cc_final: 0.8440 (ttp-110) REVERT: N 94 ASP cc_start: 0.8326 (m-30) cc_final: 0.7902 (m-30) REVERT: O 6 GLN cc_start: 0.7551 (pt0) cc_final: 0.6691 (pt0) REVERT: O 59 TYR cc_start: 0.6178 (m-80) cc_final: 0.5783 (m-80) REVERT: O 82 MET cc_start: 0.6546 (mtp) cc_final: 0.5875 (mmm) REVERT: O 100 MET cc_start: 0.8657 (mtp) cc_final: 0.8191 (mtt) REVERT: O 105 HIS cc_start: 0.7594 (p-80) cc_final: 0.7290 (m-70) REVERT: P 27 GLN cc_start: 0.6966 (mt0) cc_final: 0.6749 (mp10) REVERT: P 51 ILE cc_start: 0.7580 (mm) cc_final: 0.7348 (mm) REVERT: P 71 PHE cc_start: 0.8016 (m-80) cc_final: 0.7592 (m-10) REVERT: P 100 GLN cc_start: 0.7358 (pm20) cc_final: 0.7014 (pm20) REVERT: Q 36 TRP cc_start: 0.8691 (m100) cc_final: 0.7935 (m100) REVERT: Q 93 VAL cc_start: 0.9275 (t) cc_final: 0.9059 (m) REVERT: Q 100 MET cc_start: 0.8336 (mtp) cc_final: 0.7799 (mmt) REVERT: R 27 HIS cc_start: 0.8061 (t-90) cc_final: 0.7613 (t70) REVERT: R 38 GLN cc_start: 0.8106 (tt0) cc_final: 0.7690 (tm-30) REVERT: S 4 LEU cc_start: 0.8281 (mt) cc_final: 0.7909 (mp) REVERT: S 24 VAL cc_start: 0.8303 (t) cc_final: 0.7100 (t) REVERT: S 58 ASN cc_start: 0.7426 (t0) cc_final: 0.7123 (t0) REVERT: S 72 ASP cc_start: 0.7284 (t0) cc_final: 0.7043 (t0) REVERT: S 75 LYS cc_start: 0.8982 (mttt) cc_final: 0.8762 (mtmm) REVERT: S 78 PHE cc_start: 0.5581 (m-80) cc_final: 0.4671 (m-80) REVERT: S 107 THR cc_start: 0.8256 (t) cc_final: 0.7970 (p) outliers start: 2 outliers final: 1 residues processed: 874 average time/residue: 0.4208 time to fit residues: 540.9245 Evaluate side-chains 441 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 440 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 94 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 132 optimal weight: 0.0980 chunk 162 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 195 ASN B 577 GLN C 195 ASN C 249 HIS C 425 ASN ** E 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN E 653 GLN D 203 GLN ** D 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 653 GLN H 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 25 ASN N 35 GLN O 100 HIS ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100CASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.114529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.087394 restraints weight = 64272.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.088877 restraints weight = 38689.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090183 restraints weight = 27458.083| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24168 Z= 0.188 Angle : 0.873 20.771 33048 Z= 0.432 Chirality : 0.053 0.388 3946 Planarity : 0.006 0.056 4000 Dihedral : 12.494 82.628 5010 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.73 % Allowed : 11.93 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 2780 helix: 0.61 (0.26), residues: 397 sheet: 0.48 (0.16), residues: 882 loop : -0.09 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 338 HIS 0.014 0.002 HIS A 72 PHE 0.039 0.003 PHE O 29 TYR 0.031 0.002 TYR L 49 ARG 0.010 0.001 ARG S 100F Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 37) link_NAG-ASN : angle 2.84398 ( 111) link_ALPHA1-6 : bond 0.00924 ( 16) link_ALPHA1-6 : angle 1.70852 ( 48) link_BETA1-4 : bond 0.01499 ( 29) link_BETA1-4 : angle 4.20070 ( 87) link_ALPHA1-2 : bond 0.00681 ( 1) link_ALPHA1-2 : angle 5.86846 ( 3) link_ALPHA1-3 : bond 0.01431 ( 15) link_ALPHA1-3 : angle 2.51673 ( 45) hydrogen bonds : bond 0.05722 ( 842) hydrogen bonds : angle 6.02349 ( 2214) SS BOND : bond 0.00351 ( 43) SS BOND : angle 1.35755 ( 86) covalent geometry : bond 0.00405 (24027) covalent geometry : angle 0.82183 (32668) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 578 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8341 (m100) cc_final: 0.7667 (m100) REVERT: A 180 ASP cc_start: 0.8431 (m-30) cc_final: 0.8089 (m-30) REVERT: A 391 PHE cc_start: 0.8642 (m-80) cc_final: 0.8378 (m-10) REVERT: A 426 MET cc_start: 0.6153 (mtp) cc_final: 0.5322 (mtp) REVERT: B 530 MET cc_start: 0.2753 (mmp) cc_final: 0.2268 (mmt) REVERT: B 535 MET cc_start: 0.8387 (mmm) cc_final: 0.8154 (mmt) REVERT: B 588 ARG cc_start: 0.8897 (tmm-80) cc_final: 0.8612 (ttm-80) REVERT: B 601 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8237 (mmmt) REVERT: C 75 VAL cc_start: 0.8759 (p) cc_final: 0.8465 (m) REVERT: C 95 MET cc_start: 0.8608 (ptp) cc_final: 0.8374 (ptp) REVERT: C 112 TRP cc_start: 0.8087 (m100) cc_final: 0.7629 (m100) REVERT: C 180 ASP cc_start: 0.8790 (m-30) cc_final: 0.8492 (t0) REVERT: C 277 PHE cc_start: 0.7669 (m-80) cc_final: 0.7348 (m-10) REVERT: C 342 LEU cc_start: 0.9008 (mt) cc_final: 0.8798 (tp) REVERT: C 434 MET cc_start: 0.8923 (ttp) cc_final: 0.8616 (ttp) REVERT: E 557 ARG cc_start: 0.3694 (OUTLIER) cc_final: 0.3310 (mtt-85) REVERT: E 601 LYS cc_start: 0.8434 (mttt) cc_final: 0.7915 (mtmt) REVERT: E 618 SER cc_start: 0.7596 (m) cc_final: 0.7118 (p) REVERT: E 620 ASP cc_start: 0.8657 (p0) cc_final: 0.8316 (p0) REVERT: E 627 THR cc_start: 0.8788 (p) cc_final: 0.8552 (p) REVERT: E 638 TYR cc_start: 0.8109 (m-80) cc_final: 0.7389 (m-80) REVERT: E 639 THR cc_start: 0.8610 (m) cc_final: 0.7932 (p) REVERT: E 644 ASN cc_start: 0.8320 (m-40) cc_final: 0.8004 (m-40) REVERT: E 646 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8385 (mm) REVERT: E 647 GLU cc_start: 0.7478 (pp20) cc_final: 0.7075 (pp20) REVERT: E 648 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8238 (mt-10) REVERT: D 80 ASN cc_start: 0.7954 (p0) cc_final: 0.7742 (t0) REVERT: D 92 ASN cc_start: 0.7804 (t0) cc_final: 0.7570 (t0) REVERT: D 116 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8837 (mp) REVERT: D 425 ASN cc_start: 0.8472 (p0) cc_final: 0.7917 (p0) REVERT: D 468 PHE cc_start: 0.7946 (m-80) cc_final: 0.7664 (m-80) REVERT: F 601 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8642 (mmmm) REVERT: F 623 TRP cc_start: 0.8663 (m100) cc_final: 0.8386 (m100) REVERT: F 663 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7169 (mt) REVERT: H 36 TRP cc_start: 0.8583 (m100) cc_final: 0.7818 (m-10) REVERT: H 82 MET cc_start: 0.7259 (tpp) cc_final: 0.6445 (tpp) REVERT: H 102 TYR cc_start: 0.6864 (OUTLIER) cc_final: 0.6544 (t80) REVERT: L 4 MET cc_start: 0.6683 (mtm) cc_final: 0.6296 (mtm) REVERT: L 27 GLN cc_start: 0.7506 (tp-100) cc_final: 0.6949 (tm-30) REVERT: L 27 LEU cc_start: 0.7898 (mt) cc_final: 0.7394 (mt) REVERT: L 61 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7756 (ptp-170) REVERT: L 71 PHE cc_start: 0.8489 (m-80) cc_final: 0.7893 (m-80) REVERT: L 79 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7325 (tm-30) REVERT: L 94 PHE cc_start: 0.6422 (m-80) cc_final: 0.5983 (m-80) REVERT: L 96 TRP cc_start: 0.7596 (m-90) cc_final: 0.6309 (m-90) REVERT: M 72 ASP cc_start: 0.7943 (t0) cc_final: 0.7250 (t0) REVERT: M 86 ASP cc_start: 0.8086 (m-30) cc_final: 0.7820 (m-30) REVERT: M 87 THR cc_start: 0.9535 (t) cc_final: 0.9219 (m) REVERT: M 100 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8140 (mt-10) REVERT: M 100 MET cc_start: 0.6974 (ptp) cc_final: 0.6446 (mtt) REVERT: N 24 ASN cc_start: 0.8192 (t0) cc_final: 0.7703 (t0) REVERT: N 25 ASN cc_start: 0.8218 (m-40) cc_final: 0.7860 (m110) REVERT: N 34 TYR cc_start: 0.8147 (m-80) cc_final: 0.7772 (m-10) REVERT: N 36 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7302 (tm-30) REVERT: N 49 ASP cc_start: 0.8027 (m-30) cc_final: 0.7806 (m-30) REVERT: N 70 THR cc_start: 0.8770 (m) cc_final: 0.8499 (p) REVERT: N 71 LEU cc_start: 0.8668 (tp) cc_final: 0.8402 (tp) REVERT: N 81 GLU cc_start: 0.8591 (tt0) cc_final: 0.8033 (mt-10) REVERT: N 90 ASP cc_start: 0.8826 (t0) cc_final: 0.8233 (t0) REVERT: O 59 TYR cc_start: 0.6451 (m-80) cc_final: 0.5627 (m-80) REVERT: O 75 MET cc_start: 0.8209 (mmm) cc_final: 0.7689 (mtp) REVERT: O 82 VAL cc_start: 0.8239 (m) cc_final: 0.7895 (p) REVERT: O 100 MET cc_start: 0.8665 (mtp) cc_final: 0.8339 (mtt) REVERT: P 17 GLN cc_start: 0.8612 (tt0) cc_final: 0.8193 (mm-40) REVERT: P 27 GLN cc_start: 0.6946 (mt0) cc_final: 0.6693 (mp10) REVERT: P 50 LYS cc_start: 0.8073 (ttpp) cc_final: 0.7767 (ptmt) REVERT: P 51 ILE cc_start: 0.8582 (mm) cc_final: 0.8067 (mp) REVERT: P 71 PHE cc_start: 0.7791 (m-80) cc_final: 0.7250 (m-10) REVERT: P 81 GLU cc_start: 0.8299 (pm20) cc_final: 0.7745 (tm-30) REVERT: P 100 GLN cc_start: 0.7773 (pm20) cc_final: 0.6837 (tm-30) REVERT: Q 36 TRP cc_start: 0.8589 (m100) cc_final: 0.8178 (m100) REVERT: Q 38 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7456 (ptm160) REVERT: Q 46 GLU cc_start: 0.8277 (tt0) cc_final: 0.7915 (tt0) REVERT: R 27 HIS cc_start: 0.8182 (t-90) cc_final: 0.7784 (t-170) REVERT: R 71 PHE cc_start: 0.7872 (m-80) cc_final: 0.7290 (m-80) REVERT: R 90 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: S 24 VAL cc_start: 0.8174 (t) cc_final: 0.7700 (t) REVERT: S 58 ASN cc_start: 0.7644 (t0) cc_final: 0.7329 (t0) REVERT: S 63 LEU cc_start: 0.8669 (mt) cc_final: 0.8270 (pt) REVERT: S 72 ASP cc_start: 0.7426 (t0) cc_final: 0.6984 (t0) REVERT: S 75 LYS cc_start: 0.8983 (mttt) cc_final: 0.8781 (mtmm) REVERT: S 100 VAL cc_start: 0.9322 (t) cc_final: 0.9001 (m) REVERT: T 40 GLN cc_start: 0.7981 (mp10) cc_final: 0.7776 (mm-40) REVERT: T 104 VAL cc_start: 0.9104 (t) cc_final: 0.8836 (m) outliers start: 68 outliers final: 25 residues processed: 606 average time/residue: 0.3622 time to fit residues: 332.2163 Evaluate side-chains 445 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 413 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain E residue 557 ARG Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain Q residue 38 ARG Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 81 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 101 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 240 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN A 374 HIS A 425 ASN B 540 GLN C 195 ASN C 425 ASN E 616 ASN D 94 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN P 53 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN S 56 ASN S 100CASN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.110378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082842 restraints weight = 64900.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084479 restraints weight = 39785.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085372 restraints weight = 28762.245| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24168 Z= 0.216 Angle : 0.812 21.402 33048 Z= 0.401 Chirality : 0.050 0.327 3946 Planarity : 0.005 0.051 4000 Dihedral : 11.159 79.371 5006 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.53 % Allowed : 14.34 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.16), residues: 2780 helix: 0.57 (0.27), residues: 411 sheet: 0.25 (0.16), residues: 914 loop : -0.27 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 596 HIS 0.010 0.001 HIS A 72 PHE 0.029 0.003 PHE O 29 TYR 0.055 0.002 TYR E 643 ARG 0.008 0.001 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 37) link_NAG-ASN : angle 2.51822 ( 111) link_ALPHA1-6 : bond 0.00718 ( 16) link_ALPHA1-6 : angle 1.89312 ( 48) link_BETA1-4 : bond 0.01282 ( 29) link_BETA1-4 : angle 3.84927 ( 87) link_ALPHA1-2 : bond 0.00669 ( 1) link_ALPHA1-2 : angle 5.39233 ( 3) link_ALPHA1-3 : bond 0.01243 ( 15) link_ALPHA1-3 : angle 2.18721 ( 45) hydrogen bonds : bond 0.05214 ( 842) hydrogen bonds : angle 5.71277 ( 2214) SS BOND : bond 0.00393 ( 43) SS BOND : angle 1.22062 ( 86) covalent geometry : bond 0.00490 (24027) covalent geometry : angle 0.76679 (32668) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 449 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8174 (t) cc_final: 0.7924 (p) REVERT: A 102 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7479 (tm-30) REVERT: A 112 TRP cc_start: 0.8319 (m100) cc_final: 0.7701 (m100) REVERT: A 180 ASP cc_start: 0.8540 (m-30) cc_final: 0.8150 (m-30) REVERT: A 391 PHE cc_start: 0.8741 (m-80) cc_final: 0.8222 (m-80) REVERT: A 426 MET cc_start: 0.6264 (mtp) cc_final: 0.5651 (mtp) REVERT: B 530 MET cc_start: 0.2737 (mmp) cc_final: 0.2405 (mmt) REVERT: B 601 LYS cc_start: 0.8822 (mmtm) cc_final: 0.8184 (mmmm) REVERT: B 628 TRP cc_start: 0.2826 (m-10) cc_final: 0.2421 (m-10) REVERT: C 95 MET cc_start: 0.8690 (ptp) cc_final: 0.8382 (ptp) REVERT: C 165 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8167 (mm) REVERT: C 180 ASP cc_start: 0.8894 (m-30) cc_final: 0.8636 (t0) REVERT: C 268 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8506 (mmmt) REVERT: C 373 MET cc_start: 0.7628 (mmt) cc_final: 0.7282 (mmm) REVERT: E 601 LYS cc_start: 0.8534 (mttt) cc_final: 0.8224 (pttm) REVERT: E 631 TRP cc_start: 0.8799 (t-100) cc_final: 0.8441 (t-100) REVERT: E 644 ASN cc_start: 0.8311 (m-40) cc_final: 0.7979 (t0) REVERT: E 647 GLU cc_start: 0.7639 (pp20) cc_final: 0.7118 (pp20) REVERT: E 648 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8333 (mt-10) REVERT: D 92 ASN cc_start: 0.8458 (t0) cc_final: 0.8257 (t0) REVERT: D 116 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8694 (mp) REVERT: D 425 ASN cc_start: 0.8366 (p0) cc_final: 0.7889 (p0) REVERT: D 468 PHE cc_start: 0.8235 (m-80) cc_final: 0.7667 (m-80) REVERT: F 535 MET cc_start: 0.8647 (tpp) cc_final: 0.8294 (tpt) REVERT: F 589 ASP cc_start: 0.8927 (m-30) cc_final: 0.8724 (m-30) REVERT: F 601 LYS cc_start: 0.8979 (mmtt) cc_final: 0.8685 (mmmm) REVERT: F 623 TRP cc_start: 0.8915 (m100) cc_final: 0.8396 (m100) REVERT: F 663 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7351 (tp) REVERT: H 28 THR cc_start: 0.4777 (p) cc_final: 0.4512 (p) REVERT: H 33 TYR cc_start: 0.6975 (m-10) cc_final: 0.6766 (m-10) REVERT: H 82 MET cc_start: 0.7347 (tpp) cc_final: 0.6734 (tpp) REVERT: L 4 MET cc_start: 0.7229 (mtm) cc_final: 0.6864 (mtm) REVERT: L 27 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7370 (tm-30) REVERT: L 27 LEU cc_start: 0.8400 (mt) cc_final: 0.7709 (mt) REVERT: L 42 GLN cc_start: 0.8731 (mp10) cc_final: 0.7998 (mp10) REVERT: L 79 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7439 (tm-30) REVERT: L 94 PHE cc_start: 0.6128 (m-80) cc_final: 0.5758 (m-80) REVERT: L 96 TRP cc_start: 0.7445 (m-90) cc_final: 0.6370 (m-90) REVERT: M 47 TRP cc_start: 0.8065 (t60) cc_final: 0.7209 (t60) REVERT: M 59 TYR cc_start: 0.8444 (m-80) cc_final: 0.8199 (m-80) REVERT: M 72 ASP cc_start: 0.8061 (t0) cc_final: 0.7359 (t0) REVERT: M 86 ASP cc_start: 0.7954 (m-30) cc_final: 0.7617 (m-30) REVERT: M 100 ASN cc_start: 0.7075 (OUTLIER) cc_final: 0.6850 (p0) REVERT: N 24 ASN cc_start: 0.8222 (t0) cc_final: 0.7766 (t0) REVERT: N 25 ASN cc_start: 0.8373 (m-40) cc_final: 0.8168 (m-40) REVERT: N 34 TYR cc_start: 0.8413 (m-80) cc_final: 0.7895 (m-10) REVERT: N 49 ASP cc_start: 0.7976 (m-30) cc_final: 0.7610 (m-30) REVERT: N 50 SER cc_start: 0.8303 (p) cc_final: 0.7880 (t) REVERT: N 64 LYS cc_start: 0.7962 (ttpp) cc_final: 0.7357 (tttt) REVERT: N 70 THR cc_start: 0.8806 (m) cc_final: 0.8522 (p) REVERT: N 90 ASP cc_start: 0.9039 (t0) cc_final: 0.8485 (t0) REVERT: N 102 THR cc_start: 0.8613 (p) cc_final: 0.8354 (p) REVERT: O 59 TYR cc_start: 0.6111 (m-80) cc_final: 0.5872 (m-10) REVERT: P 17 GLN cc_start: 0.8594 (tt0) cc_final: 0.8278 (mm-40) REVERT: P 27 GLN cc_start: 0.7057 (mt0) cc_final: 0.6746 (mp10) REVERT: P 49 TYR cc_start: 0.8118 (p90) cc_final: 0.7749 (p90) REVERT: P 51 ILE cc_start: 0.8612 (mm) cc_final: 0.8244 (mp) REVERT: P 53 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7553 (t0) REVERT: P 71 PHE cc_start: 0.7742 (m-80) cc_final: 0.7350 (m-10) REVERT: P 81 GLU cc_start: 0.8590 (pm20) cc_final: 0.8079 (tm-30) REVERT: P 100 GLN cc_start: 0.7705 (pm20) cc_final: 0.6828 (tm-30) REVERT: Q 12 LEU cc_start: 0.8591 (tp) cc_final: 0.8337 (tp) REVERT: Q 36 TRP cc_start: 0.8692 (m100) cc_final: 0.8219 (m100) REVERT: Q 46 GLU cc_start: 0.8311 (tt0) cc_final: 0.7954 (tt0) REVERT: Q 100 MET cc_start: 0.7800 (mmt) cc_final: 0.7093 (mmp) REVERT: R 27 HIS cc_start: 0.8348 (t-90) cc_final: 0.7799 (t-170) REVERT: R 51 ILE cc_start: 0.8489 (mp) cc_final: 0.8252 (mm) REVERT: R 71 PHE cc_start: 0.8009 (m-80) cc_final: 0.7147 (m-80) REVERT: R 90 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.6553 (pt0) REVERT: S 24 VAL cc_start: 0.8355 (t) cc_final: 0.7970 (t) REVERT: S 58 ASN cc_start: 0.7876 (t0) cc_final: 0.7506 (t0) REVERT: S 72 ASP cc_start: 0.7557 (t0) cc_final: 0.7007 (t0) REVERT: S 75 LYS cc_start: 0.9109 (mttt) cc_final: 0.8754 (mtmm) REVERT: T 2 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8309 (mm-30) REVERT: T 18 ARG cc_start: 0.6941 (mmm160) cc_final: 0.6709 (mmm160) REVERT: T 73 ILE cc_start: 0.8990 (mt) cc_final: 0.8787 (mt) outliers start: 88 outliers final: 50 residues processed: 495 average time/residue: 0.3469 time to fit residues: 265.8468 Evaluate side-chains 446 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 100 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 48 TYR Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 127 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 178 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN E 616 ASN E 653 GLN ** D 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN F 550 GLN F 553 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 1 GLN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.110631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.083342 restraints weight = 65220.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084769 restraints weight = 39849.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.085851 restraints weight = 28261.606| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24168 Z= 0.162 Angle : 0.759 20.407 33048 Z= 0.368 Chirality : 0.049 0.303 3946 Planarity : 0.005 0.061 4000 Dihedral : 10.105 72.752 5006 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.41 % Allowed : 16.14 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2780 helix: 0.60 (0.27), residues: 405 sheet: 0.27 (0.16), residues: 912 loop : -0.40 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 69 HIS 0.006 0.001 HIS A 72 PHE 0.021 0.002 PHE L 71 TYR 0.030 0.002 TYR E 643 ARG 0.009 0.001 ARG Q 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 37) link_NAG-ASN : angle 2.27485 ( 111) link_ALPHA1-6 : bond 0.00758 ( 16) link_ALPHA1-6 : angle 1.82508 ( 48) link_BETA1-4 : bond 0.01239 ( 29) link_BETA1-4 : angle 3.52359 ( 87) link_ALPHA1-2 : bond 0.00682 ( 1) link_ALPHA1-2 : angle 5.00210 ( 3) link_ALPHA1-3 : bond 0.01209 ( 15) link_ALPHA1-3 : angle 2.06564 ( 45) hydrogen bonds : bond 0.04628 ( 842) hydrogen bonds : angle 5.59460 ( 2214) SS BOND : bond 0.00426 ( 43) SS BOND : angle 1.23762 ( 86) covalent geometry : bond 0.00364 (24027) covalent geometry : angle 0.71729 (32668) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 433 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.8212 (t) cc_final: 0.7918 (p) REVERT: A 95 MET cc_start: 0.9126 (ppp) cc_final: 0.8707 (ppp) REVERT: A 102 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7432 (tm-30) REVERT: A 180 ASP cc_start: 0.8569 (m-30) cc_final: 0.8031 (m-30) REVERT: A 338 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6329 (p-90) REVERT: A 342 LEU cc_start: 0.8717 (mt) cc_final: 0.8388 (mt) REVERT: A 391 PHE cc_start: 0.8730 (m-80) cc_final: 0.8280 (m-10) REVERT: B 530 MET cc_start: 0.2598 (mmp) cc_final: 0.2320 (mmt) REVERT: B 601 LYS cc_start: 0.8726 (mmtm) cc_final: 0.8340 (mmmt) REVERT: C 95 MET cc_start: 0.8485 (ptp) cc_final: 0.8265 (ptp) REVERT: C 165 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7978 (mm) REVERT: C 180 ASP cc_start: 0.8911 (m-30) cc_final: 0.8657 (t0) REVERT: C 373 MET cc_start: 0.7717 (mmt) cc_final: 0.7316 (mmm) REVERT: E 601 LYS cc_start: 0.8486 (mttt) cc_final: 0.8114 (mtmm) REVERT: E 621 MET cc_start: 0.8296 (ppp) cc_final: 0.8079 (ppp) REVERT: E 631 TRP cc_start: 0.8717 (t-100) cc_final: 0.8366 (t-100) REVERT: E 644 ASN cc_start: 0.8378 (m-40) cc_final: 0.7929 (t0) REVERT: E 647 GLU cc_start: 0.7702 (pp20) cc_final: 0.7087 (pp20) REVERT: E 648 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8196 (mt-10) REVERT: D 468 PHE cc_start: 0.8044 (m-80) cc_final: 0.7624 (m-80) REVERT: F 589 ASP cc_start: 0.8861 (m-30) cc_final: 0.8631 (m-30) REVERT: F 601 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8735 (mmmm) REVERT: F 623 TRP cc_start: 0.8957 (m100) cc_final: 0.8565 (m100) REVERT: F 663 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7856 (tp) REVERT: H 28 THR cc_start: 0.4278 (p) cc_final: 0.4047 (p) REVERT: H 82 MET cc_start: 0.7622 (tpp) cc_final: 0.6977 (tpp) REVERT: H 102 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.6406 (t80) REVERT: L 4 MET cc_start: 0.7214 (mtm) cc_final: 0.6900 (mtm) REVERT: L 27 GLN cc_start: 0.7759 (tp-100) cc_final: 0.7449 (tm-30) REVERT: L 27 LEU cc_start: 0.8374 (mt) cc_final: 0.7664 (mt) REVERT: L 42 GLN cc_start: 0.8737 (mp10) cc_final: 0.8108 (mp10) REVERT: L 49 TYR cc_start: 0.7454 (p90) cc_final: 0.6785 (p90) REVERT: L 77 ARG cc_start: 0.8731 (ttp-110) cc_final: 0.8231 (ttp80) REVERT: L 79 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7629 (tm-30) REVERT: L 94 PHE cc_start: 0.6035 (m-80) cc_final: 0.5705 (m-80) REVERT: L 96 TRP cc_start: 0.7445 (m-90) cc_final: 0.6470 (m-90) REVERT: M 47 TRP cc_start: 0.7954 (t60) cc_final: 0.7269 (t60) REVERT: M 59 TYR cc_start: 0.8517 (m-80) cc_final: 0.8292 (m-80) REVERT: M 72 ASP cc_start: 0.7992 (t0) cc_final: 0.7328 (t0) REVERT: M 86 ASP cc_start: 0.8029 (m-30) cc_final: 0.7621 (m-30) REVERT: M 91 TYR cc_start: 0.8057 (m-80) cc_final: 0.7555 (m-10) REVERT: M 100 MET cc_start: 0.7030 (ptp) cc_final: 0.6747 (mtt) REVERT: N 24 ASN cc_start: 0.8167 (t0) cc_final: 0.7701 (t0) REVERT: N 25 ASN cc_start: 0.8250 (m-40) cc_final: 0.7994 (m-40) REVERT: N 34 TYR cc_start: 0.8450 (m-80) cc_final: 0.7961 (m-10) REVERT: N 36 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7420 (tm-30) REVERT: N 49 ASP cc_start: 0.7986 (m-30) cc_final: 0.7634 (m-30) REVERT: N 50 SER cc_start: 0.8301 (p) cc_final: 0.7864 (t) REVERT: N 51 ASP cc_start: 0.6832 (t70) cc_final: 0.6202 (t70) REVERT: N 64 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7461 (tttt) REVERT: N 70 THR cc_start: 0.8748 (m) cc_final: 0.8460 (p) REVERT: O 59 TYR cc_start: 0.6166 (m-80) cc_final: 0.5799 (m-10) REVERT: O 75 MET cc_start: 0.8174 (mmm) cc_final: 0.7891 (mtp) REVERT: O 100 MET cc_start: 0.7958 (mtp) cc_final: 0.7306 (mmm) REVERT: P 17 GLN cc_start: 0.8517 (tt0) cc_final: 0.8282 (mm-40) REVERT: P 27 GLN cc_start: 0.7053 (mt0) cc_final: 0.6735 (mp10) REVERT: P 42 GLN cc_start: 0.8832 (mm110) cc_final: 0.8152 (tp40) REVERT: P 51 ILE cc_start: 0.8550 (mm) cc_final: 0.8035 (mp) REVERT: P 81 GLU cc_start: 0.8598 (pm20) cc_final: 0.8042 (tm-30) REVERT: P 100 GLN cc_start: 0.7508 (pm20) cc_final: 0.6739 (tm-30) REVERT: Q 36 TRP cc_start: 0.8637 (m100) cc_final: 0.8076 (m100) REVERT: Q 46 GLU cc_start: 0.8323 (tt0) cc_final: 0.8014 (tt0) REVERT: R 27 HIS cc_start: 0.8369 (t-90) cc_final: 0.7802 (t-170) REVERT: R 51 ILE cc_start: 0.8555 (mp) cc_final: 0.8352 (mm) REVERT: R 71 PHE cc_start: 0.8014 (m-80) cc_final: 0.7759 (m-80) REVERT: R 90 GLN cc_start: 0.7575 (OUTLIER) cc_final: 0.6384 (pt0) REVERT: S 58 ASN cc_start: 0.7830 (t0) cc_final: 0.7503 (t0) REVERT: S 72 ASP cc_start: 0.7769 (t0) cc_final: 0.7163 (t0) REVERT: S 75 LYS cc_start: 0.8991 (mttt) cc_final: 0.8742 (mtmm) REVERT: T 2 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7790 (pp20) REVERT: T 18 ARG cc_start: 0.7303 (mmm160) cc_final: 0.6923 (mmm160) REVERT: T 94 ASP cc_start: 0.6883 (t0) cc_final: 0.6531 (t0) outliers start: 85 outliers final: 56 residues processed: 481 average time/residue: 0.3540 time to fit residues: 262.8238 Evaluate side-chains 448 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 387 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 550 GLN Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 88 CYS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 204 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 92 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 616 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 550 GLN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 HIS ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN R 37 GLN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.107261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.080719 restraints weight = 65122.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081377 restraints weight = 40286.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082505 restraints weight = 29904.624| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24168 Z= 0.177 Angle : 0.751 20.475 33048 Z= 0.364 Chirality : 0.049 0.302 3946 Planarity : 0.005 0.050 4000 Dihedral : 9.498 68.723 5006 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.65 % Rotamer: Outliers : 3.33 % Allowed : 16.79 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2780 helix: 0.79 (0.28), residues: 388 sheet: 0.16 (0.16), residues: 936 loop : -0.44 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 596 HIS 0.006 0.001 HIS T 95 PHE 0.033 0.002 PHE T 60 TYR 0.034 0.002 TYR L 49 ARG 0.009 0.001 ARG Q 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 37) link_NAG-ASN : angle 2.19203 ( 111) link_ALPHA1-6 : bond 0.00722 ( 16) link_ALPHA1-6 : angle 1.89110 ( 48) link_BETA1-4 : bond 0.01173 ( 29) link_BETA1-4 : angle 3.43485 ( 87) link_ALPHA1-2 : bond 0.00623 ( 1) link_ALPHA1-2 : angle 5.05175 ( 3) link_ALPHA1-3 : bond 0.01174 ( 15) link_ALPHA1-3 : angle 2.02873 ( 45) hydrogen bonds : bond 0.04442 ( 842) hydrogen bonds : angle 5.52925 ( 2214) SS BOND : bond 0.00339 ( 43) SS BOND : angle 1.21029 ( 86) covalent geometry : bond 0.00401 (24027) covalent geometry : angle 0.71126 (32668) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 404 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.9118 (ppp) cc_final: 0.8652 (ppp) REVERT: A 102 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 180 ASP cc_start: 0.8596 (m-30) cc_final: 0.8179 (m-30) REVERT: A 338 TRP cc_start: 0.6796 (OUTLIER) cc_final: 0.6348 (p-90) REVERT: A 434 MET cc_start: 0.7884 (ttp) cc_final: 0.7643 (ttm) REVERT: B 530 MET cc_start: 0.2553 (mmp) cc_final: 0.2348 (mmt) REVERT: B 621 MET cc_start: 0.8016 (ptm) cc_final: 0.7723 (ppp) REVERT: C 95 MET cc_start: 0.8574 (ptp) cc_final: 0.8368 (ptp) REVERT: C 103 GLN cc_start: 0.8712 (tp40) cc_final: 0.8156 (tm-30) REVERT: C 165 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8056 (mm) REVERT: E 601 LYS cc_start: 0.8515 (mttt) cc_final: 0.8129 (mtmm) REVERT: E 621 MET cc_start: 0.8341 (ppp) cc_final: 0.8099 (ppp) REVERT: E 644 ASN cc_start: 0.8472 (m-40) cc_final: 0.8146 (t0) REVERT: E 647 GLU cc_start: 0.7768 (pp20) cc_final: 0.7296 (pp20) REVERT: D 104 MET cc_start: 0.8782 (tmm) cc_final: 0.8372 (tmm) REVERT: D 180 ASP cc_start: 0.8016 (m-30) cc_final: 0.7555 (t0) REVERT: D 468 PHE cc_start: 0.8064 (m-80) cc_final: 0.7608 (m-80) REVERT: F 589 ASP cc_start: 0.8918 (m-30) cc_final: 0.8655 (m-30) REVERT: F 601 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8724 (mmmm) REVERT: F 623 TRP cc_start: 0.9046 (m100) cc_final: 0.8617 (m100) REVERT: F 663 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7543 (tp) REVERT: H 82 MET cc_start: 0.7754 (tpp) cc_final: 0.7072 (tpp) REVERT: H 102 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6437 (t80) REVERT: L 4 MET cc_start: 0.7306 (mtm) cc_final: 0.6987 (mtm) REVERT: L 9 LEU cc_start: 0.8926 (mt) cc_final: 0.8571 (tp) REVERT: L 27 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7516 (tm-30) REVERT: L 27 LEU cc_start: 0.8398 (mt) cc_final: 0.7608 (mt) REVERT: L 42 GLN cc_start: 0.8688 (mp10) cc_final: 0.8069 (mp10) REVERT: L 49 TYR cc_start: 0.7702 (p90) cc_final: 0.7424 (p90) REVERT: L 77 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.7968 (ttp80) REVERT: L 94 PHE cc_start: 0.6077 (m-80) cc_final: 0.5721 (m-80) REVERT: L 96 TRP cc_start: 0.7500 (m-90) cc_final: 0.6569 (m-90) REVERT: M 72 ASP cc_start: 0.8052 (t0) cc_final: 0.7375 (t0) REVERT: M 86 ASP cc_start: 0.8106 (m-30) cc_final: 0.7713 (m-30) REVERT: M 91 TYR cc_start: 0.8029 (m-80) cc_final: 0.7389 (m-10) REVERT: M 95 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7801 (tm-30) REVERT: M 100 MET cc_start: 0.7268 (ptp) cc_final: 0.6959 (mtt) REVERT: M 100 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8379 (mtt180) REVERT: N 24 ASN cc_start: 0.8202 (t0) cc_final: 0.7761 (t0) REVERT: N 25 ASN cc_start: 0.8267 (m-40) cc_final: 0.8042 (m-40) REVERT: N 34 TYR cc_start: 0.8636 (m-80) cc_final: 0.8148 (m-10) REVERT: N 48 TYR cc_start: 0.7694 (t80) cc_final: 0.7422 (t80) REVERT: N 49 ASP cc_start: 0.8042 (m-30) cc_final: 0.7742 (m-30) REVERT: N 50 SER cc_start: 0.8350 (p) cc_final: 0.7901 (t) REVERT: N 51 ASP cc_start: 0.6940 (t70) cc_final: 0.6179 (t70) REVERT: N 64 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7500 (tttt) REVERT: N 70 THR cc_start: 0.8762 (m) cc_final: 0.8481 (p) REVERT: O 75 MET cc_start: 0.8180 (mmm) cc_final: 0.7900 (mtp) REVERT: P 27 GLN cc_start: 0.7080 (mt0) cc_final: 0.6751 (mp10) REVERT: P 42 GLN cc_start: 0.8825 (mm110) cc_final: 0.8240 (tp40) REVERT: P 71 PHE cc_start: 0.8232 (m-80) cc_final: 0.7601 (m-10) REVERT: P 100 GLN cc_start: 0.7512 (pm20) cc_final: 0.7220 (tm-30) REVERT: Q 46 GLU cc_start: 0.8301 (tt0) cc_final: 0.8042 (tt0) REVERT: Q 100 MET cc_start: 0.7808 (mmt) cc_final: 0.7379 (mmp) REVERT: R 27 HIS cc_start: 0.8318 (t-90) cc_final: 0.7805 (t70) REVERT: R 51 ILE cc_start: 0.8587 (mp) cc_final: 0.8381 (mm) REVERT: S 58 ASN cc_start: 0.7827 (t0) cc_final: 0.7441 (t0) REVERT: S 72 ASP cc_start: 0.7702 (t0) cc_final: 0.6985 (t0) REVERT: S 75 LYS cc_start: 0.9052 (mttt) cc_final: 0.8797 (mtmm) REVERT: T 2 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7819 (pp20) outliers start: 83 outliers final: 60 residues processed: 453 average time/residue: 0.3335 time to fit residues: 236.4949 Evaluate side-chains 439 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 375 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 148 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 193 optimal weight: 0.0000 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 HIS R 37 GLN ** T 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.107217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081006 restraints weight = 67609.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082279 restraints weight = 42403.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082876 restraints weight = 32795.127| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 24168 Z= 0.209 Angle : 0.778 20.389 33048 Z= 0.376 Chirality : 0.049 0.305 3946 Planarity : 0.005 0.052 4000 Dihedral : 9.141 64.400 5006 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 3.86 % Allowed : 17.03 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2780 helix: 0.83 (0.28), residues: 382 sheet: 0.02 (0.17), residues: 925 loop : -0.47 (0.17), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 596 HIS 0.011 0.002 HIS A 72 PHE 0.021 0.002 PHE T 60 TYR 0.024 0.002 TYR P 49 ARG 0.006 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 37) link_NAG-ASN : angle 2.22627 ( 111) link_ALPHA1-6 : bond 0.00664 ( 16) link_ALPHA1-6 : angle 1.96920 ( 48) link_BETA1-4 : bond 0.01126 ( 29) link_BETA1-4 : angle 3.41395 ( 87) link_ALPHA1-2 : bond 0.00574 ( 1) link_ALPHA1-2 : angle 5.15151 ( 3) link_ALPHA1-3 : bond 0.01127 ( 15) link_ALPHA1-3 : angle 2.07456 ( 45) hydrogen bonds : bond 0.04485 ( 842) hydrogen bonds : angle 5.51198 ( 2214) SS BOND : bond 0.00415 ( 43) SS BOND : angle 2.08344 ( 86) covalent geometry : bond 0.00480 (24027) covalent geometry : angle 0.73396 (32668) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 390 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7559 (tm-30) REVERT: A 180 ASP cc_start: 0.8564 (m-30) cc_final: 0.8183 (m-30) REVERT: A 338 TRP cc_start: 0.6814 (OUTLIER) cc_final: 0.6552 (p-90) REVERT: A 342 LEU cc_start: 0.8816 (mt) cc_final: 0.8607 (mp) REVERT: C 103 GLN cc_start: 0.8722 (tp40) cc_final: 0.8158 (tm-30) REVERT: C 165 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8248 (mm) REVERT: C 371 ILE cc_start: 0.8930 (mm) cc_final: 0.8650 (tp) REVERT: E 530 MET cc_start: 0.8716 (mmm) cc_final: 0.8393 (tpp) REVERT: E 601 LYS cc_start: 0.8493 (mttt) cc_final: 0.8117 (mtmm) REVERT: E 644 ASN cc_start: 0.8530 (m-40) cc_final: 0.8093 (m-40) REVERT: E 647 GLU cc_start: 0.7717 (pp20) cc_final: 0.7135 (pp20) REVERT: E 648 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8103 (mt-10) REVERT: D 104 MET cc_start: 0.8957 (tmm) cc_final: 0.8397 (tmm) REVERT: D 125 LEU cc_start: 0.9376 (mt) cc_final: 0.9137 (mt) REVERT: D 180 ASP cc_start: 0.7988 (m-30) cc_final: 0.7652 (t0) REVERT: D 317 PHE cc_start: 0.8382 (t80) cc_final: 0.8168 (t80) REVERT: D 434 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: D 468 PHE cc_start: 0.7990 (m-80) cc_final: 0.7249 (m-80) REVERT: F 601 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8765 (mmmm) REVERT: F 623 TRP cc_start: 0.9032 (m100) cc_final: 0.8469 (m100) REVERT: F 663 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7664 (tp) REVERT: H 82 MET cc_start: 0.7771 (tpp) cc_final: 0.7021 (tpp) REVERT: H 100 MET cc_start: 0.7759 (tpp) cc_final: 0.7357 (tpp) REVERT: H 102 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6491 (t80) REVERT: L 4 MET cc_start: 0.7578 (mtm) cc_final: 0.7112 (mtm) REVERT: L 9 LEU cc_start: 0.8924 (mt) cc_final: 0.8602 (tp) REVERT: L 27 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7570 (tm-30) REVERT: L 27 LEU cc_start: 0.8388 (mt) cc_final: 0.7570 (mt) REVERT: L 42 GLN cc_start: 0.8651 (mp10) cc_final: 0.8053 (mp10) REVERT: L 49 TYR cc_start: 0.7907 (p90) cc_final: 0.7529 (p90) REVERT: L 77 ARG cc_start: 0.8709 (ttp-110) cc_final: 0.8238 (ttp80) REVERT: L 79 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7600 (tm-30) REVERT: L 94 PHE cc_start: 0.6237 (m-80) cc_final: 0.5854 (m-80) REVERT: L 96 TRP cc_start: 0.7665 (m-90) cc_final: 0.6679 (m-90) REVERT: M 47 TRP cc_start: 0.8025 (t60) cc_final: 0.7781 (t60) REVERT: M 58 ASN cc_start: 0.7792 (t0) cc_final: 0.7277 (t0) REVERT: M 72 ASP cc_start: 0.8179 (t0) cc_final: 0.7523 (t0) REVERT: M 86 ASP cc_start: 0.8146 (m-30) cc_final: 0.7691 (m-30) REVERT: M 91 TYR cc_start: 0.8065 (m-80) cc_final: 0.7441 (m-10) REVERT: M 100 MET cc_start: 0.7274 (ptp) cc_final: 0.7040 (mtt) REVERT: N 24 ASN cc_start: 0.8185 (t0) cc_final: 0.7759 (t0) REVERT: N 25 ASN cc_start: 0.8338 (m-40) cc_final: 0.8094 (m-40) REVERT: N 34 TYR cc_start: 0.8698 (m-80) cc_final: 0.8210 (m-10) REVERT: N 36 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 48 TYR cc_start: 0.7650 (t80) cc_final: 0.7436 (t80) REVERT: N 49 ASP cc_start: 0.8069 (m-30) cc_final: 0.7791 (m-30) REVERT: N 50 SER cc_start: 0.8396 (p) cc_final: 0.7988 (t) REVERT: N 51 ASP cc_start: 0.7089 (t0) cc_final: 0.6330 (t70) REVERT: N 64 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7570 (tttt) REVERT: N 70 THR cc_start: 0.8791 (m) cc_final: 0.8528 (p) REVERT: P 27 GLN cc_start: 0.7123 (mt0) cc_final: 0.6863 (mp10) REVERT: P 42 GLN cc_start: 0.8793 (mm110) cc_final: 0.8198 (tp40) REVERT: P 51 ILE cc_start: 0.8583 (mp) cc_final: 0.8248 (mp) REVERT: P 71 PHE cc_start: 0.8413 (m-80) cc_final: 0.7668 (m-10) REVERT: Q 46 GLU cc_start: 0.8331 (tt0) cc_final: 0.8103 (tt0) REVERT: Q 100 MET cc_start: 0.7758 (mmt) cc_final: 0.7175 (mmp) REVERT: R 27 HIS cc_start: 0.8233 (t-90) cc_final: 0.7624 (t-170) REVERT: S 58 ASN cc_start: 0.7852 (t0) cc_final: 0.7537 (t0) REVERT: S 72 ASP cc_start: 0.7732 (t0) cc_final: 0.6975 (t0) REVERT: S 75 LYS cc_start: 0.9123 (mttt) cc_final: 0.8905 (mtmm) REVERT: S 100 GLU cc_start: 0.7859 (mt-10) cc_final: 0.6831 (mm-30) REVERT: T 2 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7869 (pp20) REVERT: T 48 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: T 94 ASP cc_start: 0.7027 (t0) cc_final: 0.6597 (t0) outliers start: 96 outliers final: 62 residues processed: 449 average time/residue: 0.3480 time to fit residues: 243.8778 Evaluate side-chains 433 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 365 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 548 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 72 THR Chi-restraints excluded: chain T residue 73 ILE Chi-restraints excluded: chain T residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 149 optimal weight: 20.0000 chunk 202 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 99 optimal weight: 0.0470 chunk 206 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 74 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 616 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100CASN P 6 GLN ** P 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 35 GLN T 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.081543 restraints weight = 67734.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082647 restraints weight = 41780.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083408 restraints weight = 32595.968| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24168 Z= 0.169 Angle : 0.739 20.466 33048 Z= 0.355 Chirality : 0.049 0.288 3946 Planarity : 0.005 0.052 4000 Dihedral : 8.652 59.918 5006 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 3.78 % Allowed : 17.87 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.16), residues: 2780 helix: 0.69 (0.28), residues: 389 sheet: 0.01 (0.17), residues: 960 loop : -0.50 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 596 HIS 0.007 0.001 HIS T 95 PHE 0.019 0.002 PHE T 60 TYR 0.019 0.002 TYR Q 102 ARG 0.006 0.001 ARG T 75 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 37) link_NAG-ASN : angle 2.09474 ( 111) link_ALPHA1-6 : bond 0.00697 ( 16) link_ALPHA1-6 : angle 1.85743 ( 48) link_BETA1-4 : bond 0.01126 ( 29) link_BETA1-4 : angle 3.31800 ( 87) link_ALPHA1-2 : bond 0.00560 ( 1) link_ALPHA1-2 : angle 4.98966 ( 3) link_ALPHA1-3 : bond 0.01138 ( 15) link_ALPHA1-3 : angle 2.04452 ( 45) hydrogen bonds : bond 0.04184 ( 842) hydrogen bonds : angle 5.46521 ( 2214) SS BOND : bond 0.00366 ( 43) SS BOND : angle 1.09720 ( 86) covalent geometry : bond 0.00384 (24027) covalent geometry : angle 0.70166 (32668) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 405 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7524 (t80) cc_final: 0.7305 (t80) REVERT: A 95 MET cc_start: 0.9179 (ppp) cc_final: 0.8810 (ppp) REVERT: A 102 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7584 (tm-30) REVERT: A 125 LEU cc_start: 0.9404 (mp) cc_final: 0.9158 (mt) REVERT: A 180 ASP cc_start: 0.8596 (m-30) cc_final: 0.8133 (m-30) REVERT: A 338 TRP cc_start: 0.6968 (OUTLIER) cc_final: 0.6536 (p-90) REVERT: B 577 GLN cc_start: 0.9348 (tp40) cc_final: 0.9147 (mm-40) REVERT: C 42 VAL cc_start: 0.9505 (t) cc_final: 0.9304 (p) REVERT: C 92 ASN cc_start: 0.8333 (m-40) cc_final: 0.8064 (p0) REVERT: C 103 GLN cc_start: 0.8652 (tp40) cc_final: 0.8144 (tm-30) REVERT: C 165 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 371 ILE cc_start: 0.8938 (mm) cc_final: 0.8662 (tp) REVERT: C 434 MET cc_start: 0.8953 (ttm) cc_final: 0.8721 (ttp) REVERT: E 530 MET cc_start: 0.8699 (mmm) cc_final: 0.8148 (tpp) REVERT: E 601 LYS cc_start: 0.8463 (mttt) cc_final: 0.8099 (mtmm) REVERT: E 618 SER cc_start: 0.8471 (m) cc_final: 0.8262 (m) REVERT: E 621 MET cc_start: 0.8236 (ppp) cc_final: 0.8011 (ppp) REVERT: E 644 ASN cc_start: 0.8560 (m-40) cc_final: 0.8114 (m-40) REVERT: E 647 GLU cc_start: 0.7687 (pp20) cc_final: 0.7168 (pp20) REVERT: E 648 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8085 (mt-10) REVERT: D 104 MET cc_start: 0.8950 (tmm) cc_final: 0.8399 (tmm) REVERT: D 468 PHE cc_start: 0.7927 (m-80) cc_final: 0.7142 (m-80) REVERT: F 623 TRP cc_start: 0.9101 (m100) cc_final: 0.8516 (m100) REVERT: F 663 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7588 (tp) REVERT: H 82 MET cc_start: 0.7749 (tpp) cc_final: 0.7129 (tpp) REVERT: H 100 MET cc_start: 0.7783 (tpp) cc_final: 0.7523 (tpp) REVERT: H 102 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6683 (t80) REVERT: L 4 MET cc_start: 0.7547 (mtm) cc_final: 0.7288 (mtm) REVERT: L 9 LEU cc_start: 0.8948 (mt) cc_final: 0.8557 (tp) REVERT: L 27 LEU cc_start: 0.8218 (mt) cc_final: 0.7386 (mt) REVERT: L 42 GLN cc_start: 0.8816 (mp10) cc_final: 0.8168 (mp10) REVERT: L 49 TYR cc_start: 0.8009 (p90) cc_final: 0.7554 (p90) REVERT: L 77 ARG cc_start: 0.8658 (ttp-110) cc_final: 0.8198 (ttp80) REVERT: L 79 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7606 (tm-30) REVERT: L 94 PHE cc_start: 0.6196 (m-80) cc_final: 0.5659 (m-80) REVERT: L 96 TRP cc_start: 0.7583 (m-90) cc_final: 0.6600 (m-90) REVERT: M 47 TRP cc_start: 0.7994 (t60) cc_final: 0.7697 (t60) REVERT: M 58 ASN cc_start: 0.7982 (t0) cc_final: 0.7637 (t0) REVERT: M 72 ASP cc_start: 0.8188 (t0) cc_final: 0.7528 (t0) REVERT: M 86 ASP cc_start: 0.8129 (m-30) cc_final: 0.7647 (m-30) REVERT: M 91 TYR cc_start: 0.8077 (m-80) cc_final: 0.7436 (m-10) REVERT: M 100 MET cc_start: 0.7298 (ptp) cc_final: 0.6780 (mtt) REVERT: N 24 ASN cc_start: 0.8204 (t0) cc_final: 0.7761 (t0) REVERT: N 25 ASN cc_start: 0.8342 (m-40) cc_final: 0.8127 (m-40) REVERT: N 34 TYR cc_start: 0.8691 (m-80) cc_final: 0.8202 (m-10) REVERT: N 36 GLN cc_start: 0.7699 (tm-30) cc_final: 0.7350 (tm-30) REVERT: N 49 ASP cc_start: 0.8083 (m-30) cc_final: 0.7811 (m-30) REVERT: N 50 SER cc_start: 0.8378 (p) cc_final: 0.7988 (t) REVERT: N 51 ASP cc_start: 0.7176 (t0) cc_final: 0.6363 (t70) REVERT: N 64 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7530 (tttt) REVERT: N 70 THR cc_start: 0.8777 (m) cc_final: 0.8501 (p) REVERT: N 89 TRP cc_start: 0.9204 (t-100) cc_final: 0.8906 (t-100) REVERT: P 27 GLN cc_start: 0.7097 (mt0) cc_final: 0.6850 (mp10) REVERT: P 42 GLN cc_start: 0.8740 (mm110) cc_final: 0.7978 (tm-30) REVERT: P 51 ILE cc_start: 0.8643 (mp) cc_final: 0.8326 (mp) REVERT: P 71 PHE cc_start: 0.8575 (m-80) cc_final: 0.7725 (m-10) REVERT: Q 46 GLU cc_start: 0.8227 (tt0) cc_final: 0.8020 (tt0) REVERT: Q 100 MET cc_start: 0.7725 (mmt) cc_final: 0.7217 (mmp) REVERT: R 27 HIS cc_start: 0.8266 (t-90) cc_final: 0.7657 (t70) REVERT: R 42 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7282 (mm-40) REVERT: S 58 ASN cc_start: 0.7846 (t0) cc_final: 0.7560 (t0) REVERT: S 72 ASP cc_start: 0.7653 (t0) cc_final: 0.6913 (t0) REVERT: S 75 LYS cc_start: 0.9132 (mttt) cc_final: 0.8922 (mtmm) REVERT: S 100 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6775 (mm-30) REVERT: T 48 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6221 (m-80) REVERT: T 75 ARG cc_start: 0.7950 (mtm-85) cc_final: 0.7509 (mtm-85) REVERT: T 94 ASP cc_start: 0.7006 (t0) cc_final: 0.6702 (t0) outliers start: 94 outliers final: 64 residues processed: 461 average time/residue: 0.3515 time to fit residues: 251.8218 Evaluate side-chains 443 residues out of total 2490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 72 HIS Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 338 TRP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 636 ASP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain C residue 53 PHE Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain E residue 584 GLU Chi-restraints excluded: chain E residue 603 ILE Chi-restraints excluded: chain E residue 629 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain H residue 102 TYR Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 73 THR Chi-restraints excluded: chain M residue 82 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 32 HIS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 87 GLN Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LYS Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain Q residue 32 HIS Chi-restraints excluded: chain Q residue 53 TRP Chi-restraints excluded: chain Q residue 110 LEU Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 90 GLN Chi-restraints excluded: chain R residue 102 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain T residue 20 THR Chi-restraints excluded: chain T residue 21 CYS Chi-restraints excluded: chain T residue 32 HIS Chi-restraints excluded: chain T residue 48 TYR Chi-restraints excluded: chain T residue 73 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0069 > 50: distance: 18 - 154: 18.685 distance: 21 - 151: 5.512 distance: 85 - 179: 20.641 distance: 94 - 161: 34.928 distance: 97 - 158: 10.855 distance: 109 - 148: 7.883 distance: 112 - 145: 20.710 distance: 132 - 138: 9.114 distance: 138 - 139: 13.009 distance: 139 - 140: 9.202 distance: 139 - 142: 9.991 distance: 140 - 141: 8.128 distance: 140 - 145: 14.804 distance: 142 - 143: 5.804 distance: 142 - 144: 23.512 distance: 145 - 146: 8.861 distance: 146 - 147: 16.201 distance: 146 - 149: 15.565 distance: 147 - 148: 8.341 distance: 147 - 151: 5.407 distance: 149 - 150: 8.415 distance: 152 - 153: 18.213 distance: 152 - 155: 15.222 distance: 153 - 154: 9.868 distance: 153 - 158: 12.241 distance: 155 - 156: 18.265 distance: 155 - 157: 14.114 distance: 158 - 159: 5.411 distance: 159 - 160: 10.476 distance: 159 - 162: 16.317 distance: 160 - 161: 15.909 distance: 160 - 165: 21.272 distance: 162 - 163: 16.647 distance: 162 - 164: 18.105 distance: 165 - 166: 23.338 distance: 166 - 167: 23.201 distance: 166 - 169: 14.833 distance: 167 - 168: 8.423 distance: 167 - 174: 12.553 distance: 169 - 170: 11.975 distance: 170 - 171: 16.820 distance: 171 - 172: 3.880 distance: 171 - 173: 14.570 distance: 175 - 178: 9.292 distance: 176 - 180: 7.790 distance: 178 - 179: 25.241 distance: 180 - 181: 3.066 distance: 181 - 182: 12.226 distance: 181 - 184: 11.079 distance: 182 - 183: 15.387 distance: 182 - 187: 9.436 distance: 184 - 185: 7.618 distance: 184 - 186: 7.842 distance: 187 - 188: 7.545 distance: 188 - 189: 8.827 distance: 188 - 191: 5.612 distance: 189 - 190: 14.084 distance: 189 - 197: 5.597 distance: 191 - 192: 3.135 distance: 192 - 193: 15.879 distance: 192 - 194: 3.691 distance: 193 - 195: 12.039 distance: 194 - 196: 10.101 distance: 195 - 196: 9.538 distance: 197 - 198: 28.790 distance: 198 - 199: 11.317 distance: 199 - 200: 20.229 distance: 199 - 201: 14.879 distance: 201 - 202: 8.072 distance: 202 - 203: 12.035 distance: 202 - 205: 19.290 distance: 203 - 204: 8.537 distance: 205 - 206: 17.680 distance: 205 - 207: 9.274 distance: 206 - 208: 4.326