Starting phenix.real_space_refine on Sun Aug 24 06:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnh_41416/08_2025/8tnh_41416.map" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 123 5.16 5 C 11001 2.51 5 N 2988 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} 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: "K" 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: "L" 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.32, per 1000 atoms: 0.24 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.53, 133.2, 126.54, 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 123 16.00 O 3555 8.00 N 2988 7.00 C 11001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 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=2.05 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=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 197 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 197 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 197 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 295 " " NAG c 1 " - " ASN E 332 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 386 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 783.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3926 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 44 sheets defined 19.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.106A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.685A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.969A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.465A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.863A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.721A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.990A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.024A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.683A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.004A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.096A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 597 removed outlier: 3.617A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.862A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR D 643 " --> pdb=" O THR D 639 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.032A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.835A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.820A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.714A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.628A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.783A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.838A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.728A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.929A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.635A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.676A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.667A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.729A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.666A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.290A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.432A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 272 removed outlier: 7.871A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 272 removed outlier: 10.142A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 5.398A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.632A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.552A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.228A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.513A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 174 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 272 Processing sheet with id=AC1, first strand: chain 'C' and resid 377 through 378 removed outlier: 3.542A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.807A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.744A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.410A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.214A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 161 through 162 removed outlier: 3.785A pdb=" N MET E 161 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 272 Processing sheet with id=AD3, first strand: chain 'E' and resid 416 through 417 removed outlier: 3.628A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 308 through 312 removed outlier: 4.387A pdb=" N GLY E 312 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN E 315 " --> pdb=" O GLY E 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.745A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 378 removed outlier: 3.540A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 423 through 424 removed outlier: 3.853A pdb=" N ILE E 424 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG H 38 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR H 94 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR I 94 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR J 94 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3272 1.33 - 1.46: 6720 1.46 - 1.60: 7837 1.60 - 1.74: 2 1.74 - 1.88: 160 Bond restraints: 17991 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.331 1.365 -0.034 7.90e-03 1.60e+04 1.82e+01 bond pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.58e-02 4.01e+03 1.81e+01 bond pdb=" C TYR A 318 " pdb=" O TYR A 318 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.19e-02 7.06e+03 1.41e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.462 0.072 1.93e-02 2.68e+03 1.41e+01 bond pdb=" C TYR E 318 " pdb=" O TYR E 318 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.26e-02 6.30e+03 9.81e+00 ... (remaining 17986 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 24208 3.29 - 6.57: 183 6.57 - 9.86: 15 9.86 - 13.14: 4 13.14 - 16.43: 1 Bond angle restraints: 24411 Sorted by residual: angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 130.83 -16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" C LYS C 155 " pdb=" N ASN C 156 " pdb=" CA ASN C 156 " ideal model delta sigma weight residual 122.93 114.23 8.70 1.45e+00 4.76e-01 3.60e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.28 -12.88 2.30e+00 1.89e-01 3.14e+01 angle pdb=" C ASN C 160 " pdb=" CA ASN C 160 " pdb=" CB ASN C 160 " ideal model delta sigma weight residual 111.70 118.28 -6.58 1.31e+00 5.83e-01 2.52e+01 angle pdb=" N CYS C 296 " pdb=" CA CYS C 296 " pdb=" C CYS C 296 " ideal model delta sigma weight residual 108.42 115.74 -7.32 1.54e+00 4.22e-01 2.26e+01 ... (remaining 24406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 10351 21.70 - 43.40: 1176 43.40 - 65.09: 237 65.09 - 86.79: 59 86.79 - 108.49: 18 Dihedral angle restraints: 11841 sinusoidal: 5754 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -173.47 87.47 1 1.00e+01 1.00e-02 9.18e+01 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 -4.82 -81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N MET C 161 " pdb=" CA MET C 161 " ideal model delta harmonic sigma weight residual -180.00 -142.88 -37.12 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 11838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 2947 0.238 - 0.476: 14 0.476 - 0.715: 0 0.715 - 0.953: 0 0.953 - 1.191: 1 Chirality restraints: 2962 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP E 321A" pdb=" N ASP E 321A" pdb=" C ASP E 321A" pdb=" CB ASP E 321A" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2959 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 160 " 0.067 2.00e-02 2.50e+03 6.03e-02 4.55e+01 pdb=" CG ASN C 160 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 160 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 160 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.042 2.00e-02 2.50e+03 3.98e-02 1.98e+01 pdb=" CG ASN C 156 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.038 2.00e-02 2.50e+03 3.59e-02 1.61e+01 pdb=" CG ASN A 339 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.040 2.00e-02 2.50e+03 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1246 2.73 - 3.27: 16167 3.27 - 3.82: 25524 3.82 - 4.36: 29141 4.36 - 4.90: 53977 Nonbonded interactions: 126055 Sorted by model distance: nonbonded pdb=" O SER C 375 " pdb=" OG SER C 375 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG B 617 " pdb=" OE1 GLU B 634 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.222 3.040 nonbonded pdb=" N GLU C 49 " pdb=" OE1 GLU C 49 " model vdw 2.244 3.120 nonbonded pdb=" O SER E 375 " pdb=" OG SER E 375 " model vdw 2.251 3.040 ... (remaining 126050 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' and resid 31 through 607) selection = chain 'C' selection = (chain 'E' and resid 31 through 607) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.940 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.005 0.073 18106 Z= 0.251 Angle : 0.847 18.862 24717 Z= 0.421 Chirality : 0.057 1.191 2962 Planarity : 0.004 0.055 3042 Dihedral : 18.142 108.487 7798 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.05 % Favored : 90.71 % Rotamer: Outliers : 0.48 % Allowed : 32.14 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 2077 helix: 1.96 (0.31), residues: 333 sheet: -0.75 (0.21), residues: 654 loop : -1.99 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 151 TYR 0.017 0.001 TYR C 484 PHE 0.023 0.001 PHE J 98 TRP 0.013 0.001 TRP D 596 HIS 0.003 0.001 HIS J 100C Details of bonding type rmsd covalent geometry : bond 0.00495 (17991) covalent geometry : angle 0.77282 (24411) SS BOND : bond 0.00625 ( 39) SS BOND : angle 2.33432 ( 78) hydrogen bonds : bond 0.12875 ( 534) hydrogen bonds : angle 4.87930 ( 1413) link_ALPHA1-3 : bond 0.00571 ( 2) link_ALPHA1-3 : angle 2.91189 ( 6) link_BETA1-4 : bond 0.00600 ( 25) link_BETA1-4 : angle 1.51379 ( 75) link_NAG-ASN : bond 0.00611 ( 49) link_NAG-ASN : angle 4.11761 ( 147) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 335 time to evaluate : 0.709 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: A 107 ASP cc_start: 0.7559 (t0) cc_final: 0.7012 (t0) REVERT: B 588 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6331 (ttm-80) REVERT: C 478 ASN cc_start: 0.8427 (m-40) cc_final: 0.8095 (t0) REVERT: H 79 TYR cc_start: 0.8715 (m-80) cc_final: 0.8140 (m-80) REVERT: H 95 ASP cc_start: 0.8524 (t0) cc_final: 0.8314 (m-30) REVERT: I 18 LEU cc_start: 0.8503 (mt) cc_final: 0.8203 (mp) REVERT: I 79 TYR cc_start: 0.8513 (m-80) cc_final: 0.8094 (m-80) REVERT: J 28 ASP cc_start: 0.8240 (p0) cc_final: 0.7389 (p0) REVERT: J 79 TYR cc_start: 0.8656 (m-80) cc_final: 0.8015 (m-80) outliers start: 9 outliers final: 2 residues processed: 342 average time/residue: 0.1723 time to fit residues: 84.2309 Evaluate side-chains 201 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 199 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain I residue 50 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 258 GLN A 293 GLN A 348 GLN C 67 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 293 GLN C 302 ASN C 348 GLN C 411 ASN D 625 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN F 590 GLN F 591 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82BASN I 97 GLN J 57 GLN J 82BASN J 97 GLN J 108 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.037920 restraints weight = 79838.890| |-----------------------------------------------------------------------------| r_work (start): 0.2634 rms_B_bonded: 6.15 r_work: 0.2458 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18106 Z= 0.155 Angle : 0.748 13.664 24717 Z= 0.369 Chirality : 0.047 0.334 2962 Planarity : 0.004 0.040 3042 Dihedral : 10.302 76.388 3852 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.57 % Favored : 91.29 % Rotamer: Outliers : 4.45 % Allowed : 30.10 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.19), residues: 2077 helix: 2.05 (0.29), residues: 337 sheet: -0.85 (0.21), residues: 624 loop : -1.70 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 327 TYR 0.016 0.001 TYR H 60 PHE 0.015 0.001 PHE A 382 TRP 0.017 0.001 TRP C 69 HIS 0.006 0.001 HIS J 100C Details of bonding type rmsd covalent geometry : bond 0.00358 (17991) covalent geometry : angle 0.70104 (24411) SS BOND : bond 0.00557 ( 39) SS BOND : angle 1.96460 ( 78) hydrogen bonds : bond 0.04022 ( 534) hydrogen bonds : angle 4.45701 ( 1413) link_ALPHA1-3 : bond 0.00756 ( 2) link_ALPHA1-3 : angle 3.06112 ( 6) link_BETA1-4 : bond 0.00373 ( 25) link_BETA1-4 : angle 1.47876 ( 75) link_NAG-ASN : bond 0.00496 ( 49) link_NAG-ASN : angle 2.98347 ( 147) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 222 time to evaluate : 0.711 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: A 69 TRP cc_start: 0.9454 (OUTLIER) cc_final: 0.8882 (m100) REVERT: A 95 MET cc_start: 0.9771 (ptm) cc_final: 0.9521 (ppp) REVERT: A 107 ASP cc_start: 0.9406 (t0) cc_final: 0.9079 (m-30) REVERT: A 150 MET cc_start: 0.9289 (mtp) cc_final: 0.9020 (mtp) REVERT: B 543 ASN cc_start: 0.9551 (t0) cc_final: 0.9341 (t0) REVERT: B 574 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8678 (pttm) REVERT: B 589 ASP cc_start: 0.9247 (m-30) cc_final: 0.8794 (p0) REVERT: B 632 ASP cc_start: 0.9739 (t0) cc_final: 0.9241 (p0) REVERT: C 42 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8214 (p) REVERT: C 104 MET cc_start: 0.9501 (ttm) cc_final: 0.9205 (ttp) REVERT: C 185 ASN cc_start: 0.8331 (t0) cc_final: 0.7818 (t0) REVERT: C 323 ILE cc_start: 0.9666 (OUTLIER) cc_final: 0.9191 (pt) REVERT: C 370 GLU cc_start: 0.9215 (mp0) cc_final: 0.8798 (mp0) REVERT: C 381 GLU cc_start: 0.7902 (mp0) cc_final: 0.7695 (mp0) REVERT: C 427 TRP cc_start: 0.9360 (m100) cc_final: 0.8929 (m100) REVERT: D 530 MET cc_start: 0.9432 (mmm) cc_final: 0.9087 (mmm) REVERT: D 589 ASP cc_start: 0.9351 (m-30) cc_final: 0.8843 (p0) REVERT: D 626 MET cc_start: 0.8994 (tpp) cc_final: 0.8682 (tpp) REVERT: D 648 GLU cc_start: 0.9534 (pp20) cc_final: 0.9331 (pp20) REVERT: E 100 MET cc_start: 0.9410 (mtt) cc_final: 0.9189 (mtt) REVERT: E 104 MET cc_start: 0.9097 (ttp) cc_final: 0.8691 (tmm) REVERT: E 185 ASN cc_start: 0.8030 (t0) cc_final: 0.7810 (t0) REVERT: E 426 MET cc_start: 0.8748 (ttp) cc_final: 0.8468 (ptt) REVERT: F 589 ASP cc_start: 0.9265 (m-30) cc_final: 0.8794 (p0) REVERT: F 626 MET cc_start: 0.8663 (tpp) cc_final: 0.8462 (tpp) REVERT: F 648 GLU cc_start: 0.9398 (pp20) cc_final: 0.9092 (pp20) REVERT: F 657 GLU cc_start: 0.9465 (tm-30) cc_final: 0.9198 (tm-30) REVERT: F 661 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9000 (pp) REVERT: H 60 TYR cc_start: 0.9371 (m-80) cc_final: 0.9031 (m-80) REVERT: H 105 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8292 (tm-30) REVERT: I 3 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8420 (tm-30) REVERT: I 18 LEU cc_start: 0.8612 (mt) cc_final: 0.8095 (mp) REVERT: I 82 MET cc_start: 0.9550 (mpp) cc_final: 0.8969 (mpp) REVERT: I 82 ASP cc_start: 0.9527 (m-30) cc_final: 0.9243 (p0) REVERT: I 82 ASN cc_start: 0.9704 (OUTLIER) cc_final: 0.9180 (t0) REVERT: J 3 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8469 (tm-30) REVERT: J 28 ASP cc_start: 0.9122 (p0) cc_final: 0.8830 (p0) REVERT: J 30 GLU cc_start: 0.8668 (mp0) cc_final: 0.8333 (mp0) REVERT: J 86 ASP cc_start: 0.9160 (m-30) cc_final: 0.8851 (m-30) REVERT: J 96 ARG cc_start: 0.9621 (mtp85) cc_final: 0.9399 (mtp85) outliers start: 83 outliers final: 28 residues processed: 299 average time/residue: 0.1487 time to fit residues: 66.4977 Evaluate side-chains 229 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 82 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 205 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.036588 restraints weight = 81886.757| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 6.11 r_work: 0.2412 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18106 Z= 0.189 Angle : 0.725 16.724 24717 Z= 0.357 Chirality : 0.046 0.270 2962 Planarity : 0.004 0.041 3042 Dihedral : 9.036 59.258 3851 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.38 % Favored : 91.48 % Rotamer: Outliers : 4.24 % Allowed : 29.88 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.19), residues: 2077 helix: 2.22 (0.29), residues: 340 sheet: -0.77 (0.21), residues: 657 loop : -1.63 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 585 TYR 0.013 0.001 TYR E 61 PHE 0.016 0.001 PHE A 382 TRP 0.019 0.001 TRP E 479 HIS 0.005 0.001 HIS J 100C Details of bonding type rmsd covalent geometry : bond 0.00433 (17991) covalent geometry : angle 0.68156 (24411) SS BOND : bond 0.00597 ( 39) SS BOND : angle 2.12365 ( 78) hydrogen bonds : bond 0.03953 ( 534) hydrogen bonds : angle 4.35546 ( 1413) link_ALPHA1-3 : bond 0.00600 ( 2) link_ALPHA1-3 : angle 2.76303 ( 6) link_BETA1-4 : bond 0.00305 ( 25) link_BETA1-4 : angle 1.45248 ( 75) link_NAG-ASN : bond 0.00453 ( 49) link_NAG-ASN : angle 2.72824 ( 147) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 211 time to evaluate : 0.601 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: A 80 ASN cc_start: 0.9776 (t0) cc_final: 0.9416 (p0) REVERT: A 95 MET cc_start: 0.9768 (ptm) cc_final: 0.9378 (ppp) REVERT: A 104 MET cc_start: 0.9102 (tmm) cc_final: 0.8691 (tmm) REVERT: A 107 ASP cc_start: 0.9480 (t0) cc_final: 0.9141 (m-30) REVERT: A 150 MET cc_start: 0.9308 (mtp) cc_final: 0.8989 (mtp) REVERT: B 543 ASN cc_start: 0.9622 (t0) cc_final: 0.9398 (t0) REVERT: B 589 ASP cc_start: 0.9280 (m-30) cc_final: 0.8793 (p0) REVERT: B 626 MET cc_start: 0.8572 (tpp) cc_final: 0.8353 (tpp) REVERT: B 632 ASP cc_start: 0.9741 (t0) cc_final: 0.9242 (p0) REVERT: B 654 GLU cc_start: 0.9356 (pp20) cc_final: 0.9102 (pp20) REVERT: B 655 LYS cc_start: 0.9536 (tppt) cc_final: 0.9301 (ptpt) REVERT: C 42 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8431 (p) REVERT: C 100 MET cc_start: 0.9452 (mtm) cc_final: 0.9039 (mtt) REVERT: C 185 ASN cc_start: 0.7944 (t0) cc_final: 0.7590 (t0) REVERT: C 323 ILE cc_start: 0.9672 (OUTLIER) cc_final: 0.9126 (pt) REVERT: C 369 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9127 (tt) REVERT: D 530 MET cc_start: 0.9296 (mmm) cc_final: 0.9045 (mmm) REVERT: D 589 ASP cc_start: 0.9336 (m-30) cc_final: 0.8899 (p0) REVERT: D 626 MET cc_start: 0.9019 (tpp) cc_final: 0.8800 (mmm) REVERT: E 54 CYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7300 (t) REVERT: E 87 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.9100 (mp0) REVERT: E 100 MET cc_start: 0.9487 (mtt) cc_final: 0.9221 (mtt) REVERT: E 104 MET cc_start: 0.9342 (ttp) cc_final: 0.9023 (tmm) REVERT: E 150 MET cc_start: 0.9553 (tpp) cc_final: 0.9167 (tpp) REVERT: E 185 ASN cc_start: 0.8161 (t0) cc_final: 0.7860 (t0) REVERT: F 584 GLU cc_start: 0.9590 (tt0) cc_final: 0.9197 (pp20) REVERT: F 589 ASP cc_start: 0.9299 (m-30) cc_final: 0.8884 (p0) REVERT: F 626 MET cc_start: 0.8645 (tpp) cc_final: 0.8385 (tpp) REVERT: F 648 GLU cc_start: 0.9306 (pp20) cc_final: 0.9034 (pp20) REVERT: F 657 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9218 (tm-30) REVERT: F 661 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9004 (pp) REVERT: H 60 TYR cc_start: 0.9333 (m-80) cc_final: 0.9082 (m-80) REVERT: H 80 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8875 (tp) REVERT: H 82 MET cc_start: 0.9319 (mpp) cc_final: 0.8974 (mpp) REVERT: I 3 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8320 (tm-30) REVERT: I 82 MET cc_start: 0.9519 (mpp) cc_final: 0.9090 (mpp) REVERT: I 95 ASP cc_start: 0.9399 (m-30) cc_final: 0.8965 (m-30) REVERT: I 101 GLN cc_start: 0.9369 (mp10) cc_final: 0.8952 (mp10) REVERT: J 28 ASP cc_start: 0.9145 (p0) cc_final: 0.8885 (p0) REVERT: J 30 GLU cc_start: 0.8699 (mp0) cc_final: 0.8497 (mp0) REVERT: J 44 GLU cc_start: 0.8774 (tp30) cc_final: 0.8503 (tm-30) REVERT: J 46 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8650 (pm20) REVERT: J 86 ASP cc_start: 0.9218 (m-30) cc_final: 0.8939 (m-30) outliers start: 79 outliers final: 45 residues processed: 283 average time/residue: 0.1332 time to fit residues: 56.3836 Evaluate side-chains 247 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 369 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 651 ASN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 478 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.035606 restraints weight = 83429.726| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 6.13 r_work: 0.2387 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 18106 Z= 0.197 Angle : 0.717 16.658 24717 Z= 0.353 Chirality : 0.045 0.255 2962 Planarity : 0.004 0.041 3042 Dihedral : 8.112 59.953 3851 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.05 % Favored : 90.90 % Rotamer: Outliers : 4.29 % Allowed : 29.99 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.19), residues: 2077 helix: 2.35 (0.30), residues: 340 sheet: -0.75 (0.21), residues: 663 loop : -1.59 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 327 TYR 0.015 0.001 TYR J 79 PHE 0.018 0.001 PHE C 159 TRP 0.018 0.001 TRP E 479 HIS 0.004 0.001 HIS J 100C Details of bonding type rmsd covalent geometry : bond 0.00452 (17991) covalent geometry : angle 0.67605 (24411) SS BOND : bond 0.00617 ( 39) SS BOND : angle 2.19423 ( 78) hydrogen bonds : bond 0.03854 ( 534) hydrogen bonds : angle 4.28440 ( 1413) link_ALPHA1-3 : bond 0.00834 ( 2) link_ALPHA1-3 : angle 2.80934 ( 6) link_BETA1-4 : bond 0.00273 ( 25) link_BETA1-4 : angle 1.39285 ( 75) link_NAG-ASN : bond 0.00454 ( 49) link_NAG-ASN : angle 2.56962 ( 147) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9771 (t0) cc_final: 0.9351 (p0) REVERT: A 95 MET cc_start: 0.9772 (ptm) cc_final: 0.9392 (ppp) REVERT: A 150 MET cc_start: 0.9306 (mtp) cc_final: 0.8980 (mtp) REVERT: A 185 ASN cc_start: 0.8962 (t0) cc_final: 0.8661 (t0) REVERT: A 278 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9252 (p) REVERT: B 543 ASN cc_start: 0.9639 (t0) cc_final: 0.9380 (t0) REVERT: B 589 ASP cc_start: 0.9316 (m-30) cc_final: 0.8834 (p0) REVERT: B 605 CYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8206 (t) REVERT: B 626 MET cc_start: 0.8585 (tpp) cc_final: 0.8257 (tpp) REVERT: B 632 ASP cc_start: 0.9745 (t0) cc_final: 0.9214 (p0) REVERT: C 42 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 69 TRP cc_start: 0.8854 (m-90) cc_final: 0.8330 (m-90) REVERT: C 95 MET cc_start: 0.9558 (ppp) cc_final: 0.9330 (ppp) REVERT: C 104 MET cc_start: 0.9594 (ttp) cc_final: 0.9222 (tmm) REVERT: C 150 MET cc_start: 0.9441 (mtm) cc_final: 0.8813 (mtt) REVERT: C 161 MET cc_start: 0.9473 (tpp) cc_final: 0.9247 (tpp) REVERT: C 185 ASN cc_start: 0.7966 (t0) cc_final: 0.7584 (t0) REVERT: C 323 ILE cc_start: 0.9680 (OUTLIER) cc_final: 0.9152 (pt) REVERT: C 370 GLU cc_start: 0.9214 (mp0) cc_final: 0.8568 (mp0) REVERT: C 381 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8240 (mm-30) REVERT: C 426 MET cc_start: 0.9014 (ttp) cc_final: 0.8549 (ptt) REVERT: C 427 TRP cc_start: 0.9457 (m100) cc_final: 0.9002 (m100) REVERT: D 589 ASP cc_start: 0.9333 (m-30) cc_final: 0.8920 (p0) REVERT: E 54 CYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7402 (t) REVERT: E 87 GLU cc_start: 0.9396 (OUTLIER) cc_final: 0.9134 (mp0) REVERT: E 95 MET cc_start: 0.9531 (ppp) cc_final: 0.9291 (ppp) REVERT: E 104 MET cc_start: 0.9381 (ttp) cc_final: 0.9063 (tmm) REVERT: E 114 GLN cc_start: 0.9660 (OUTLIER) cc_final: 0.9397 (tm-30) REVERT: E 150 MET cc_start: 0.9558 (tpp) cc_final: 0.9299 (mpp) REVERT: E 185 ASN cc_start: 0.8243 (t0) cc_final: 0.7899 (t0) REVERT: F 584 GLU cc_start: 0.9622 (tt0) cc_final: 0.9154 (pt0) REVERT: F 626 MET cc_start: 0.8614 (tpp) cc_final: 0.8314 (tpt) REVERT: F 648 GLU cc_start: 0.9371 (pp20) cc_final: 0.9117 (pp20) REVERT: F 657 GLU cc_start: 0.9521 (tm-30) cc_final: 0.9222 (tm-30) REVERT: F 661 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9001 (pp) REVERT: H 60 TYR cc_start: 0.9344 (m-80) cc_final: 0.9125 (m-80) REVERT: H 80 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8899 (tp) REVERT: H 82 MET cc_start: 0.9406 (mpp) cc_final: 0.8830 (mpp) REVERT: H 95 ASP cc_start: 0.9495 (m-30) cc_final: 0.9273 (m-30) REVERT: I 3 GLN cc_start: 0.8738 (tm-30) cc_final: 0.8283 (tm-30) REVERT: I 25 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8750 (p) REVERT: I 74 GLU cc_start: 0.9476 (pp20) cc_final: 0.9235 (pp20) REVERT: I 82 MET cc_start: 0.9541 (mpp) cc_final: 0.8983 (mpp) REVERT: I 101 GLN cc_start: 0.9376 (mp10) cc_final: 0.8963 (mp10) REVERT: J 3 GLN cc_start: 0.8803 (tm-30) cc_final: 0.8513 (tm-30) REVERT: J 22 CYS cc_start: 0.8263 (t) cc_final: 0.7867 (t) REVERT: J 46 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8569 (pm20) REVERT: J 82 ASP cc_start: 0.9394 (m-30) cc_final: 0.8583 (p0) REVERT: J 86 ASP cc_start: 0.9274 (m-30) cc_final: 0.9006 (m-30) outliers start: 80 outliers final: 51 residues processed: 267 average time/residue: 0.1376 time to fit residues: 55.1589 Evaluate side-chains 248 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 96 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.035678 restraints weight = 83854.591| |-----------------------------------------------------------------------------| r_work (start): 0.2575 rms_B_bonded: 6.11 r_work: 0.2392 rms_B_bonded: 6.09 restraints_weight: 2.0000 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 18106 Z= 0.169 Angle : 0.699 15.699 24717 Z= 0.347 Chirality : 0.045 0.248 2962 Planarity : 0.004 0.041 3042 Dihedral : 7.636 59.470 3849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.57 % Favored : 91.33 % Rotamer: Outliers : 3.86 % Allowed : 31.01 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 2077 helix: 2.36 (0.30), residues: 330 sheet: -0.72 (0.21), residues: 660 loop : -1.53 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 585 TYR 0.015 0.001 TYR J 60 PHE 0.015 0.001 PHE C 159 TRP 0.012 0.001 TRP E 479 HIS 0.003 0.001 HIS J 100C Details of bonding type rmsd covalent geometry : bond 0.00393 (17991) covalent geometry : angle 0.66145 (24411) SS BOND : bond 0.00515 ( 39) SS BOND : angle 2.06657 ( 78) hydrogen bonds : bond 0.03772 ( 534) hydrogen bonds : angle 4.24801 ( 1413) link_ALPHA1-3 : bond 0.00813 ( 2) link_ALPHA1-3 : angle 2.81154 ( 6) link_BETA1-4 : bond 0.00316 ( 25) link_BETA1-4 : angle 1.32166 ( 75) link_NAG-ASN : bond 0.00396 ( 49) link_NAG-ASN : angle 2.43904 ( 147) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 203 time to evaluate : 0.736 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 80 ASN cc_start: 0.9765 (t0) cc_final: 0.9320 (p0) REVERT: A 95 MET cc_start: 0.9780 (ptm) cc_final: 0.9400 (ppp) REVERT: A 104 MET cc_start: 0.9104 (tmm) cc_final: 0.8767 (tmm) REVERT: A 150 MET cc_start: 0.9290 (mtp) cc_final: 0.8934 (mtp) REVERT: A 278 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9240 (p) REVERT: A 479 TRP cc_start: 0.9151 (m-10) cc_final: 0.8887 (m-10) REVERT: B 543 ASN cc_start: 0.9635 (t0) cc_final: 0.9388 (t0) REVERT: B 546 SER cc_start: 0.8443 (t) cc_final: 0.8109 (m) REVERT: B 589 ASP cc_start: 0.9304 (m-30) cc_final: 0.8811 (p0) REVERT: B 605 CYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8110 (t) REVERT: B 626 MET cc_start: 0.8559 (tpp) cc_final: 0.8151 (tpp) REVERT: B 632 ASP cc_start: 0.9739 (t0) cc_final: 0.9207 (p0) REVERT: B 655 LYS cc_start: 0.9604 (tppt) cc_final: 0.9402 (tppt) REVERT: C 42 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 69 TRP cc_start: 0.8961 (m-90) cc_final: 0.8311 (m-90) REVERT: C 95 MET cc_start: 0.9565 (ppp) cc_final: 0.9299 (ppp) REVERT: C 100 MET cc_start: 0.9563 (mtm) cc_final: 0.9012 (mtt) REVERT: C 104 MET cc_start: 0.9594 (ttp) cc_final: 0.9233 (tmm) REVERT: C 150 MET cc_start: 0.9466 (mtm) cc_final: 0.8823 (mtm) REVERT: C 185 ASN cc_start: 0.8052 (t0) cc_final: 0.7665 (t0) REVERT: C 370 GLU cc_start: 0.9216 (mp0) cc_final: 0.8530 (mp0) REVERT: C 381 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8183 (mm-30) REVERT: C 426 MET cc_start: 0.9044 (ttp) cc_final: 0.8718 (ptt) REVERT: C 427 TRP cc_start: 0.9411 (m100) cc_final: 0.9005 (m100) REVERT: D 584 GLU cc_start: 0.9639 (tt0) cc_final: 0.9236 (tm-30) REVERT: D 589 ASP cc_start: 0.9340 (m-30) cc_final: 0.8894 (p0) REVERT: D 602 LEU cc_start: 0.9211 (mt) cc_final: 0.8806 (pp) REVERT: D 626 MET cc_start: 0.9094 (tpp) cc_final: 0.8426 (tmm) REVERT: D 633 LYS cc_start: 0.9525 (ptpp) cc_final: 0.9260 (pttm) REVERT: E 54 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7387 (t) REVERT: E 87 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9189 (mp0) REVERT: E 95 MET cc_start: 0.9563 (ppp) cc_final: 0.9282 (ppp) REVERT: E 100 MET cc_start: 0.9674 (mtp) cc_final: 0.9414 (mtt) REVERT: E 104 MET cc_start: 0.9399 (ttp) cc_final: 0.9137 (tmm) REVERT: E 150 MET cc_start: 0.9568 (tpp) cc_final: 0.9332 (mpp) REVERT: E 185 ASN cc_start: 0.8379 (t0) cc_final: 0.8015 (t0) REVERT: F 584 GLU cc_start: 0.9605 (tt0) cc_final: 0.9167 (pt0) REVERT: F 589 ASP cc_start: 0.9358 (m-30) cc_final: 0.8955 (p0) REVERT: F 626 MET cc_start: 0.8727 (tpp) cc_final: 0.8515 (tpp) REVERT: F 648 GLU cc_start: 0.9379 (pp20) cc_final: 0.9076 (pp20) REVERT: F 657 GLU cc_start: 0.9544 (tm-30) cc_final: 0.9265 (tm-30) REVERT: F 661 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8970 (pp) REVERT: H 47 GLU cc_start: 0.9288 (pm20) cc_final: 0.8656 (mp0) REVERT: H 80 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8817 (tp) REVERT: H 82 MET cc_start: 0.9453 (mpp) cc_final: 0.8824 (mpp) REVERT: H 102 TYR cc_start: 0.9378 (m-80) cc_final: 0.8588 (m-10) REVERT: I 3 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8253 (tm-30) REVERT: I 25 SER cc_start: 0.9094 (OUTLIER) cc_final: 0.8860 (p) REVERT: I 74 GLU cc_start: 0.9460 (pp20) cc_final: 0.9241 (pp20) REVERT: I 80 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8482 (tp) REVERT: I 82 MET cc_start: 0.9513 (mpp) cc_final: 0.9010 (mpp) REVERT: I 95 ASP cc_start: 0.9439 (m-30) cc_final: 0.9059 (m-30) REVERT: I 101 GLN cc_start: 0.9408 (mp10) cc_final: 0.8969 (mp10) REVERT: J 22 CYS cc_start: 0.8345 (t) cc_final: 0.7942 (t) REVERT: J 28 ASP cc_start: 0.9215 (p0) cc_final: 0.9009 (p0) REVERT: J 44 GLU cc_start: 0.8682 (tp30) cc_final: 0.8408 (tm-30) REVERT: J 46 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8582 (pm20) REVERT: J 47 GLU cc_start: 0.9236 (pm20) cc_final: 0.9018 (pm20) REVERT: J 86 ASP cc_start: 0.9369 (m-30) cc_final: 0.9106 (m-30) outliers start: 72 outliers final: 48 residues processed: 264 average time/residue: 0.1474 time to fit residues: 58.2350 Evaluate side-chains 247 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 161 optimal weight: 0.0870 chunk 162 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 164 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.035766 restraints weight = 84072.930| |-----------------------------------------------------------------------------| r_work (start): 0.2578 rms_B_bonded: 6.18 r_work: 0.2395 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 18106 Z= 0.148 Angle : 0.690 15.342 24717 Z= 0.341 Chirality : 0.045 0.242 2962 Planarity : 0.004 0.043 3042 Dihedral : 7.319 58.839 3849 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.47 % Favored : 91.43 % Rotamer: Outliers : 4.45 % Allowed : 30.31 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.19), residues: 2077 helix: 2.26 (0.29), residues: 342 sheet: -0.64 (0.21), residues: 648 loop : -1.50 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 585 TYR 0.029 0.001 TYR H 102 PHE 0.014 0.001 PHE C 159 TRP 0.017 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00350 (17991) covalent geometry : angle 0.65472 (24411) SS BOND : bond 0.00655 ( 39) SS BOND : angle 2.04933 ( 78) hydrogen bonds : bond 0.03612 ( 534) hydrogen bonds : angle 4.19186 ( 1413) link_ALPHA1-3 : bond 0.00759 ( 2) link_ALPHA1-3 : angle 2.74187 ( 6) link_BETA1-4 : bond 0.00325 ( 25) link_BETA1-4 : angle 1.27325 ( 75) link_NAG-ASN : bond 0.00371 ( 49) link_NAG-ASN : angle 2.34644 ( 147) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 205 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8042 (p) REVERT: A 95 MET cc_start: 0.9780 (ptm) cc_final: 0.9416 (ppp) REVERT: A 104 MET cc_start: 0.9131 (tmm) cc_final: 0.8633 (tmm) REVERT: A 150 MET cc_start: 0.9309 (mtp) cc_final: 0.8935 (mtp) REVERT: A 278 THR cc_start: 0.9516 (OUTLIER) cc_final: 0.9214 (p) REVERT: A 479 TRP cc_start: 0.9165 (m-10) cc_final: 0.8810 (m-10) REVERT: B 543 ASN cc_start: 0.9643 (t0) cc_final: 0.9388 (t0) REVERT: B 546 SER cc_start: 0.8498 (t) cc_final: 0.8270 (m) REVERT: B 589 ASP cc_start: 0.9333 (m-30) cc_final: 0.8876 (p0) REVERT: B 632 ASP cc_start: 0.9735 (t0) cc_final: 0.9214 (p0) REVERT: B 654 GLU cc_start: 0.9399 (pp20) cc_final: 0.9137 (pp20) REVERT: B 655 LYS cc_start: 0.9629 (tppt) cc_final: 0.9427 (ptpt) REVERT: C 42 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 69 TRP cc_start: 0.8987 (m-90) cc_final: 0.8272 (m-90) REVERT: C 95 MET cc_start: 0.9591 (ppp) cc_final: 0.9310 (ppp) REVERT: C 100 MET cc_start: 0.9580 (mtm) cc_final: 0.9006 (mtt) REVERT: C 104 MET cc_start: 0.9589 (ttp) cc_final: 0.9232 (tmm) REVERT: C 150 MET cc_start: 0.9505 (mtm) cc_final: 0.8923 (mtm) REVERT: C 161 MET cc_start: 0.9491 (tpp) cc_final: 0.9281 (tpp) REVERT: C 185 ASN cc_start: 0.8023 (t0) cc_final: 0.7663 (t0) REVERT: C 370 GLU cc_start: 0.9224 (mp0) cc_final: 0.8477 (mp0) REVERT: C 381 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8150 (mm-30) REVERT: D 543 ASN cc_start: 0.9396 (m110) cc_final: 0.8871 (t0) REVERT: D 589 ASP cc_start: 0.9333 (m-30) cc_final: 0.8880 (p0) REVERT: D 626 MET cc_start: 0.9027 (tpp) cc_final: 0.8348 (tmm) REVERT: E 54 CYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7387 (t) REVERT: E 87 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9212 (mp0) REVERT: E 95 MET cc_start: 0.9590 (ppp) cc_final: 0.9295 (ppp) REVERT: E 100 MET cc_start: 0.9667 (mtp) cc_final: 0.9407 (mtt) REVERT: E 104 MET cc_start: 0.9401 (ttp) cc_final: 0.9180 (tmm) REVERT: E 114 GLN cc_start: 0.9649 (OUTLIER) cc_final: 0.9371 (tm-30) REVERT: E 150 MET cc_start: 0.9571 (tpp) cc_final: 0.9345 (mpp) REVERT: E 185 ASN cc_start: 0.8413 (t0) cc_final: 0.8040 (t0) REVERT: F 584 GLU cc_start: 0.9605 (tt0) cc_final: 0.9151 (pt0) REVERT: F 589 ASP cc_start: 0.9350 (m-30) cc_final: 0.8991 (p0) REVERT: F 626 MET cc_start: 0.8677 (tpp) cc_final: 0.8449 (tpp) REVERT: F 648 GLU cc_start: 0.9387 (pp20) cc_final: 0.9128 (pp20) REVERT: F 657 GLU cc_start: 0.9527 (tm-30) cc_final: 0.9242 (tm-30) REVERT: F 661 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8946 (pp) REVERT: H 18 LEU cc_start: 0.9079 (tp) cc_final: 0.8586 (tp) REVERT: H 80 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8698 (tp) REVERT: H 82 MET cc_start: 0.9483 (mpp) cc_final: 0.8817 (mpp) REVERT: H 102 TYR cc_start: 0.9238 (m-80) cc_final: 0.8790 (m-10) REVERT: I 3 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8240 (tm-30) REVERT: I 25 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8876 (p) REVERT: I 28 ASP cc_start: 0.9114 (p0) cc_final: 0.8879 (p0) REVERT: I 29 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9315 (m) REVERT: I 74 GLU cc_start: 0.9458 (pp20) cc_final: 0.9225 (pp20) REVERT: I 80 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8515 (tp) REVERT: I 82 MET cc_start: 0.9496 (mpp) cc_final: 0.8700 (mpp) REVERT: I 101 GLN cc_start: 0.9401 (mp10) cc_final: 0.8988 (mp10) REVERT: J 22 CYS cc_start: 0.8307 (t) cc_final: 0.7905 (t) REVERT: J 44 GLU cc_start: 0.8765 (tp30) cc_final: 0.8437 (tm-30) REVERT: J 46 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8608 (pm20) REVERT: J 86 ASP cc_start: 0.9423 (m-30) cc_final: 0.9059 (m-30) outliers start: 83 outliers final: 49 residues processed: 276 average time/residue: 0.1260 time to fit residues: 52.6750 Evaluate side-chains 256 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 120 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 166 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.035962 restraints weight = 81757.766| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 6.18 r_work: 0.2411 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 18106 Z= 0.130 Angle : 0.684 14.990 24717 Z= 0.340 Chirality : 0.045 0.248 2962 Planarity : 0.004 0.044 3042 Dihedral : 7.017 59.108 3849 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Rotamer: Outliers : 3.54 % Allowed : 31.33 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.19), residues: 2077 helix: 2.27 (0.29), residues: 342 sheet: -0.60 (0.21), residues: 663 loop : -1.46 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 617 TYR 0.014 0.001 TYR J 79 PHE 0.013 0.001 PHE C 159 TRP 0.014 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00315 (17991) covalent geometry : angle 0.65397 (24411) SS BOND : bond 0.00586 ( 39) SS BOND : angle 1.95042 ( 78) hydrogen bonds : bond 0.03389 ( 534) hydrogen bonds : angle 4.11655 ( 1413) link_ALPHA1-3 : bond 0.00860 ( 2) link_ALPHA1-3 : angle 2.68576 ( 6) link_BETA1-4 : bond 0.00349 ( 25) link_BETA1-4 : angle 1.22707 ( 75) link_NAG-ASN : bond 0.00350 ( 49) link_NAG-ASN : angle 2.14219 ( 147) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 212 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7978 (p) REVERT: A 80 ASN cc_start: 0.9740 (t0) cc_final: 0.9263 (p0) REVERT: A 95 MET cc_start: 0.9759 (ptm) cc_final: 0.9399 (ppp) REVERT: A 104 MET cc_start: 0.9140 (tmm) cc_final: 0.8704 (tmm) REVERT: A 121 LYS cc_start: 0.9207 (ttmm) cc_final: 0.8934 (ttmm) REVERT: A 150 MET cc_start: 0.9318 (mtp) cc_final: 0.8926 (mtp) REVERT: A 278 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9191 (p) REVERT: A 479 TRP cc_start: 0.9202 (m-10) cc_final: 0.8871 (m-10) REVERT: B 543 ASN cc_start: 0.9622 (t0) cc_final: 0.9353 (t0) REVERT: B 589 ASP cc_start: 0.9339 (m-30) cc_final: 0.8872 (p0) REVERT: B 605 CYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8199 (t) REVERT: B 638 TYR cc_start: 0.9310 (m-10) cc_final: 0.8855 (m-10) REVERT: B 654 GLU cc_start: 0.9410 (pp20) cc_final: 0.9136 (pp20) REVERT: B 655 LYS cc_start: 0.9659 (tppt) cc_final: 0.9439 (ptpt) REVERT: C 42 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8101 (p) REVERT: C 69 TRP cc_start: 0.9016 (m-90) cc_final: 0.8321 (m-90) REVERT: C 95 MET cc_start: 0.9591 (ppp) cc_final: 0.9292 (ppp) REVERT: C 100 MET cc_start: 0.9574 (mtm) cc_final: 0.8978 (mtt) REVERT: C 104 MET cc_start: 0.9591 (ttp) cc_final: 0.9238 (tmm) REVERT: C 150 MET cc_start: 0.9519 (mtm) cc_final: 0.8913 (mtm) REVERT: C 161 MET cc_start: 0.9555 (tpp) cc_final: 0.9328 (tpp) REVERT: C 185 ASN cc_start: 0.8038 (t0) cc_final: 0.7680 (t0) REVERT: C 370 GLU cc_start: 0.9219 (mp0) cc_final: 0.8638 (mp0) REVERT: C 381 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8116 (mm-30) REVERT: D 543 ASN cc_start: 0.9410 (m110) cc_final: 0.8934 (t0) REVERT: D 589 ASP cc_start: 0.9349 (m-30) cc_final: 0.8886 (p0) REVERT: D 602 LEU cc_start: 0.9209 (mt) cc_final: 0.8799 (pp) REVERT: D 626 MET cc_start: 0.9050 (tpp) cc_final: 0.8318 (tmm) REVERT: D 633 LYS cc_start: 0.9528 (ptpp) cc_final: 0.9230 (pttm) REVERT: D 654 GLU cc_start: 0.9469 (pp20) cc_final: 0.9097 (pp20) REVERT: E 54 CYS cc_start: 0.7472 (OUTLIER) cc_final: 0.6832 (t) REVERT: E 87 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9196 (mp0) REVERT: E 95 MET cc_start: 0.9591 (ppp) cc_final: 0.9275 (ppp) REVERT: E 100 MET cc_start: 0.9681 (mtp) cc_final: 0.9439 (mtt) REVERT: E 104 MET cc_start: 0.9395 (ttp) cc_final: 0.9191 (tmm) REVERT: E 114 GLN cc_start: 0.9635 (OUTLIER) cc_final: 0.9362 (tm-30) REVERT: E 150 MET cc_start: 0.9572 (tpp) cc_final: 0.9334 (mpp) REVERT: E 185 ASN cc_start: 0.8460 (t0) cc_final: 0.8090 (t0) REVERT: F 584 GLU cc_start: 0.9600 (tt0) cc_final: 0.9139 (pt0) REVERT: F 589 ASP cc_start: 0.9329 (m-30) cc_final: 0.8910 (p0) REVERT: F 648 GLU cc_start: 0.9382 (pp20) cc_final: 0.9110 (pp20) REVERT: F 657 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9226 (tm-30) REVERT: F 661 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8911 (pp) REVERT: H 18 LEU cc_start: 0.9114 (tp) cc_final: 0.8681 (tp) REVERT: H 47 GLU cc_start: 0.9312 (pm20) cc_final: 0.8715 (mp0) REVERT: H 80 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8685 (tp) REVERT: H 82 MET cc_start: 0.9486 (mpp) cc_final: 0.8779 (mpp) REVERT: H 102 TYR cc_start: 0.9259 (m-80) cc_final: 0.8911 (m-10) REVERT: I 3 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8287 (tm-30) REVERT: I 25 SER cc_start: 0.9085 (OUTLIER) cc_final: 0.8831 (p) REVERT: I 74 GLU cc_start: 0.9467 (pp20) cc_final: 0.9220 (pp20) REVERT: I 80 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8539 (tp) REVERT: I 82 MET cc_start: 0.9484 (mpp) cc_final: 0.8692 (mpp) REVERT: I 95 ASP cc_start: 0.9470 (m-30) cc_final: 0.9078 (m-30) REVERT: I 101 GLN cc_start: 0.9421 (mp10) cc_final: 0.8980 (mp10) REVERT: J 22 CYS cc_start: 0.8319 (t) cc_final: 0.7921 (t) REVERT: J 44 GLU cc_start: 0.8715 (tp30) cc_final: 0.8388 (tm-30) REVERT: J 46 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8552 (pm20) REVERT: J 82 ASP cc_start: 0.9424 (t0) cc_final: 0.9188 (m-30) REVERT: J 86 ASP cc_start: 0.9431 (m-30) cc_final: 0.9062 (m-30) REVERT: J 102 TYR cc_start: 0.9084 (m-80) cc_final: 0.8571 (m-80) outliers start: 66 outliers final: 44 residues processed: 270 average time/residue: 0.1416 time to fit residues: 57.7213 Evaluate side-chains 259 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 204 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 130 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 105 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 440 GLN J 82BASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.046821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.034270 restraints weight = 85708.280| |-----------------------------------------------------------------------------| r_work (start): 0.2535 rms_B_bonded: 6.18 r_work: 0.2347 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 18106 Z= 0.257 Angle : 0.759 14.673 24717 Z= 0.373 Chirality : 0.045 0.256 2962 Planarity : 0.004 0.050 3042 Dihedral : 7.087 57.691 3849 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.58 % Favored : 90.32 % Rotamer: Outliers : 4.29 % Allowed : 30.95 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.19), residues: 2077 helix: 2.32 (0.29), residues: 341 sheet: -0.57 (0.21), residues: 636 loop : -1.50 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 585 TYR 0.018 0.002 TYR H 102 PHE 0.017 0.001 PHE A 382 TRP 0.019 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00578 (17991) covalent geometry : angle 0.72724 (24411) SS BOND : bond 0.00570 ( 39) SS BOND : angle 2.15292 ( 78) hydrogen bonds : bond 0.04068 ( 534) hydrogen bonds : angle 4.32485 ( 1413) link_ALPHA1-3 : bond 0.00749 ( 2) link_ALPHA1-3 : angle 2.55775 ( 6) link_BETA1-4 : bond 0.00179 ( 25) link_BETA1-4 : angle 1.39108 ( 75) link_NAG-ASN : bond 0.00498 ( 49) link_NAG-ASN : angle 2.31340 ( 147) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 193 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 95 MET cc_start: 0.9753 (ptm) cc_final: 0.9398 (ppp) REVERT: A 104 MET cc_start: 0.9167 (tmm) cc_final: 0.8774 (tmm) REVERT: A 107 ASP cc_start: 0.9581 (t0) cc_final: 0.9174 (m-30) REVERT: A 150 MET cc_start: 0.9370 (mtp) cc_final: 0.8997 (mtp) REVERT: A 278 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9198 (p) REVERT: B 543 ASN cc_start: 0.9645 (t0) cc_final: 0.9426 (t0) REVERT: B 605 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8124 (t) REVERT: B 626 MET cc_start: 0.8453 (tpt) cc_final: 0.7898 (tpp) REVERT: B 638 TYR cc_start: 0.9359 (m-10) cc_final: 0.8886 (m-10) REVERT: C 42 VAL cc_start: 0.8794 (OUTLIER) cc_final: 0.8552 (p) REVERT: C 69 TRP cc_start: 0.9058 (m-90) cc_final: 0.8225 (m-90) REVERT: C 95 MET cc_start: 0.9595 (ppp) cc_final: 0.9299 (ppp) REVERT: C 104 MET cc_start: 0.9658 (ttp) cc_final: 0.9283 (ttp) REVERT: C 150 MET cc_start: 0.9524 (mtm) cc_final: 0.8965 (mtm) REVERT: C 185 ASN cc_start: 0.8317 (t0) cc_final: 0.7977 (t0) REVERT: C 370 GLU cc_start: 0.9272 (mp0) cc_final: 0.8689 (mp0) REVERT: C 381 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8192 (mm-30) REVERT: D 542 ARG cc_start: 0.9575 (ttp80) cc_final: 0.9365 (ttp-110) REVERT: D 543 ASN cc_start: 0.9428 (m110) cc_final: 0.8943 (t0) REVERT: D 584 GLU cc_start: 0.9678 (tt0) cc_final: 0.9237 (tm-30) REVERT: D 589 ASP cc_start: 0.9381 (m-30) cc_final: 0.8935 (p0) REVERT: D 626 MET cc_start: 0.9197 (tpp) cc_final: 0.8571 (mmm) REVERT: D 633 LYS cc_start: 0.9584 (ptpp) cc_final: 0.9290 (pttm) REVERT: D 654 GLU cc_start: 0.9472 (pp20) cc_final: 0.9211 (pp20) REVERT: E 54 CYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7349 (t) REVERT: E 87 GLU cc_start: 0.9485 (OUTLIER) cc_final: 0.9266 (mp0) REVERT: E 95 MET cc_start: 0.9588 (ppp) cc_final: 0.9270 (ppp) REVERT: E 114 GLN cc_start: 0.9672 (OUTLIER) cc_final: 0.9352 (tm-30) REVERT: E 150 MET cc_start: 0.9581 (tpp) cc_final: 0.9368 (mpp) REVERT: E 185 ASN cc_start: 0.8612 (t0) cc_final: 0.8259 (t0) REVERT: E 231 LYS cc_start: 0.9779 (OUTLIER) cc_final: 0.9532 (mmtm) REVERT: E 271 MET cc_start: 0.9157 (mmm) cc_final: 0.8708 (mmp) REVERT: F 589 ASP cc_start: 0.9372 (m-30) cc_final: 0.9015 (p0) REVERT: F 626 MET cc_start: 0.8906 (tpp) cc_final: 0.8235 (tpp) REVERT: F 648 GLU cc_start: 0.9408 (pp20) cc_final: 0.9159 (pp20) REVERT: F 657 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9246 (tm-30) REVERT: F 661 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8981 (pp) REVERT: H 18 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8642 (tp) REVERT: H 47 GLU cc_start: 0.9388 (pm20) cc_final: 0.8789 (mp0) REVERT: H 80 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8759 (tp) REVERT: H 82 MET cc_start: 0.9506 (mpp) cc_final: 0.8800 (mpp) REVERT: H 102 TYR cc_start: 0.9198 (m-80) cc_final: 0.8791 (m-10) REVERT: I 3 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8036 (tm-30) REVERT: I 22 CYS cc_start: 0.8259 (t) cc_final: 0.7859 (t) REVERT: I 25 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8710 (p) REVERT: I 80 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8445 (tp) REVERT: I 82 MET cc_start: 0.9438 (mpp) cc_final: 0.8912 (mpp) REVERT: I 101 GLN cc_start: 0.9424 (mp10) cc_final: 0.8923 (mp10) REVERT: J 22 CYS cc_start: 0.8436 (t) cc_final: 0.8081 (t) REVERT: J 28 ASP cc_start: 0.9257 (p0) cc_final: 0.9027 (p0) REVERT: J 82 ASP cc_start: 0.9473 (t0) cc_final: 0.9208 (m-30) REVERT: J 86 ASP cc_start: 0.9470 (m-30) cc_final: 0.9098 (m-30) outliers start: 80 outliers final: 56 residues processed: 262 average time/residue: 0.1404 time to fit residues: 55.6962 Evaluate side-chains 258 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 47 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 133 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 169 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.035076 restraints weight = 85296.832| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 6.24 r_work: 0.2380 rms_B_bonded: 6.19 restraints_weight: 2.0000 r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 18106 Z= 0.145 Angle : 0.726 14.340 24717 Z= 0.361 Chirality : 0.045 0.247 2962 Planarity : 0.004 0.053 3042 Dihedral : 6.856 58.546 3849 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.04 % Favored : 91.86 % Rotamer: Outliers : 3.59 % Allowed : 32.08 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.19), residues: 2077 helix: 2.26 (0.29), residues: 341 sheet: -0.53 (0.21), residues: 654 loop : -1.46 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 585 TYR 0.018 0.001 TYR H 102 PHE 0.013 0.001 PHE A 382 TRP 0.023 0.001 TRP A 427 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00349 (17991) covalent geometry : angle 0.69778 (24411) SS BOND : bond 0.00587 ( 39) SS BOND : angle 2.11058 ( 78) hydrogen bonds : bond 0.03622 ( 534) hydrogen bonds : angle 4.19712 ( 1413) link_ALPHA1-3 : bond 0.00817 ( 2) link_ALPHA1-3 : angle 2.56982 ( 6) link_BETA1-4 : bond 0.00323 ( 25) link_BETA1-4 : angle 1.20303 ( 75) link_NAG-ASN : bond 0.00368 ( 49) link_NAG-ASN : angle 2.09502 ( 147) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 205 time to evaluate : 0.693 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: A 42 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8126 (p) REVERT: A 95 MET cc_start: 0.9760 (ptm) cc_final: 0.9388 (ppp) REVERT: A 150 MET cc_start: 0.9320 (mtp) cc_final: 0.9103 (mtp) REVERT: A 278 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9160 (p) REVERT: B 543 ASN cc_start: 0.9621 (t0) cc_final: 0.9399 (t0) REVERT: B 638 TYR cc_start: 0.9337 (m-10) cc_final: 0.8854 (m-10) REVERT: B 654 GLU cc_start: 0.9358 (pp20) cc_final: 0.9014 (pp20) REVERT: B 655 LYS cc_start: 0.9565 (tppt) cc_final: 0.9348 (ptpp) REVERT: C 42 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8315 (p) REVERT: C 69 TRP cc_start: 0.9075 (m-90) cc_final: 0.8240 (m-90) REVERT: C 95 MET cc_start: 0.9605 (ppp) cc_final: 0.9293 (ppp) REVERT: C 104 MET cc_start: 0.9615 (ttp) cc_final: 0.9261 (tmm) REVERT: C 150 MET cc_start: 0.9523 (mtm) cc_final: 0.8998 (mtm) REVERT: C 185 ASN cc_start: 0.8269 (t0) cc_final: 0.7911 (t0) REVERT: C 370 GLU cc_start: 0.9231 (mp0) cc_final: 0.8631 (mp0) REVERT: C 381 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 543 ASN cc_start: 0.9358 (m110) cc_final: 0.9022 (t0) REVERT: D 584 GLU cc_start: 0.9666 (tt0) cc_final: 0.9218 (tm-30) REVERT: D 589 ASP cc_start: 0.9387 (m-30) cc_final: 0.8925 (p0) REVERT: D 602 LEU cc_start: 0.9259 (mt) cc_final: 0.8815 (pp) REVERT: D 626 MET cc_start: 0.9133 (tpp) cc_final: 0.8375 (tmm) REVERT: D 633 LYS cc_start: 0.9541 (ptpp) cc_final: 0.9234 (pttm) REVERT: D 654 GLU cc_start: 0.9484 (pp20) cc_final: 0.9114 (pp20) REVERT: D 655 LYS cc_start: 0.9437 (ptpp) cc_final: 0.9199 (ptpp) REVERT: E 54 CYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7112 (t) REVERT: E 87 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9228 (mp0) REVERT: E 95 MET cc_start: 0.9599 (ppp) cc_final: 0.9269 (ppp) REVERT: E 114 GLN cc_start: 0.9658 (OUTLIER) cc_final: 0.9351 (tm-30) REVERT: E 185 ASN cc_start: 0.8565 (t0) cc_final: 0.8209 (t0) REVERT: E 271 MET cc_start: 0.9103 (mmm) cc_final: 0.8681 (mmp) REVERT: F 584 GLU cc_start: 0.9615 (tt0) cc_final: 0.9165 (pt0) REVERT: F 589 ASP cc_start: 0.9371 (m-30) cc_final: 0.8998 (p0) REVERT: F 626 MET cc_start: 0.8861 (tpp) cc_final: 0.8227 (tpp) REVERT: F 648 GLU cc_start: 0.9397 (pp20) cc_final: 0.9145 (pp20) REVERT: F 657 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9280 (tm-30) REVERT: F 661 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.8951 (pp) REVERT: H 18 LEU cc_start: 0.9083 (tp) cc_final: 0.8622 (tp) REVERT: H 47 GLU cc_start: 0.9370 (pm20) cc_final: 0.8785 (mp0) REVERT: H 80 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8658 (tp) REVERT: H 82 MET cc_start: 0.9495 (mpp) cc_final: 0.8857 (mpp) REVERT: H 102 TYR cc_start: 0.9115 (m-80) cc_final: 0.8736 (m-10) REVERT: I 3 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8283 (tm-30) REVERT: I 25 SER cc_start: 0.9092 (OUTLIER) cc_final: 0.8847 (p) REVERT: I 80 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8389 (tp) REVERT: I 82 MET cc_start: 0.9436 (mpp) cc_final: 0.8895 (mpp) REVERT: I 95 ASP cc_start: 0.9460 (m-30) cc_final: 0.9033 (m-30) REVERT: I 101 GLN cc_start: 0.9440 (mp10) cc_final: 0.8970 (mp10) REVERT: J 22 CYS cc_start: 0.8480 (t) cc_final: 0.8082 (t) REVERT: J 82 ASP cc_start: 0.9441 (t0) cc_final: 0.9028 (m-30) REVERT: J 82 ASN cc_start: 0.9784 (OUTLIER) cc_final: 0.9033 (t0) REVERT: J 86 ASP cc_start: 0.9474 (m-30) cc_final: 0.9101 (m-30) outliers start: 67 outliers final: 50 residues processed: 266 average time/residue: 0.1345 time to fit residues: 54.3582 Evaluate side-chains 261 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 102 optimal weight: 0.0670 chunk 193 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 543 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.035272 restraints weight = 84610.630| |-----------------------------------------------------------------------------| r_work (start): 0.2574 rms_B_bonded: 6.16 r_work: 0.2389 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 18106 Z= 0.149 Angle : 0.748 15.311 24717 Z= 0.370 Chirality : 0.045 0.250 2962 Planarity : 0.004 0.054 3042 Dihedral : 6.722 58.258 3849 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.67 % Rotamer: Outliers : 3.38 % Allowed : 32.46 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.19), residues: 2077 helix: 2.19 (0.29), residues: 341 sheet: -0.50 (0.21), residues: 654 loop : -1.45 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 585 TYR 0.017 0.001 TYR H 102 PHE 0.051 0.001 PHE F 519 TRP 0.020 0.001 TRP D 596 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00360 (17991) covalent geometry : angle 0.72212 (24411) SS BOND : bond 0.00571 ( 39) SS BOND : angle 2.02952 ( 78) hydrogen bonds : bond 0.03553 ( 534) hydrogen bonds : angle 4.16948 ( 1413) link_ALPHA1-3 : bond 0.00816 ( 2) link_ALPHA1-3 : angle 2.51036 ( 6) link_BETA1-4 : bond 0.00310 ( 25) link_BETA1-4 : angle 1.20802 ( 75) link_NAG-ASN : bond 0.00351 ( 49) link_NAG-ASN : angle 2.08496 ( 147) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 204 time to evaluate : 0.559 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 42 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8036 (p) REVERT: A 95 MET cc_start: 0.9749 (ptm) cc_final: 0.9379 (ppp) REVERT: A 107 ASP cc_start: 0.9574 (t0) cc_final: 0.9140 (m-30) REVERT: A 150 MET cc_start: 0.9322 (mtp) cc_final: 0.9101 (mtp) REVERT: A 278 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9145 (p) REVERT: A 479 TRP cc_start: 0.9218 (m-10) cc_final: 0.8930 (m-10) REVERT: B 543 ASN cc_start: 0.9639 (t0) cc_final: 0.9415 (t0) REVERT: B 602 LEU cc_start: 0.8956 (mt) cc_final: 0.8729 (tt) REVERT: B 638 TYR cc_start: 0.9342 (m-10) cc_final: 0.8880 (m-10) REVERT: B 654 GLU cc_start: 0.9349 (pp20) cc_final: 0.9064 (pp20) REVERT: B 655 LYS cc_start: 0.9598 (tppt) cc_final: 0.9388 (ptpp) REVERT: C 42 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 69 TRP cc_start: 0.9101 (m-90) cc_final: 0.8248 (m-90) REVERT: C 95 MET cc_start: 0.9615 (ppp) cc_final: 0.9303 (ppp) REVERT: C 104 MET cc_start: 0.9626 (ttp) cc_final: 0.9270 (tmm) REVERT: C 150 MET cc_start: 0.9520 (mtm) cc_final: 0.9025 (mtm) REVERT: C 185 ASN cc_start: 0.8280 (t0) cc_final: 0.7933 (t0) REVERT: C 370 GLU cc_start: 0.9218 (mp0) cc_final: 0.8632 (mp0) REVERT: C 381 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8100 (mm-30) REVERT: D 542 ARG cc_start: 0.9579 (ttp80) cc_final: 0.9352 (ttp-110) REVERT: D 543 ASN cc_start: 0.9383 (m-40) cc_final: 0.9011 (t0) REVERT: D 584 GLU cc_start: 0.9668 (tt0) cc_final: 0.9215 (tm-30) REVERT: D 589 ASP cc_start: 0.9383 (m-30) cc_final: 0.8918 (p0) REVERT: D 602 LEU cc_start: 0.9260 (mt) cc_final: 0.8810 (pp) REVERT: D 626 MET cc_start: 0.9142 (tpp) cc_final: 0.8423 (tmm) REVERT: D 633 LYS cc_start: 0.9549 (ptpp) cc_final: 0.9242 (pttm) REVERT: D 654 GLU cc_start: 0.9458 (pp20) cc_final: 0.9138 (pp20) REVERT: E 54 CYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6976 (t) REVERT: E 87 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9234 (mp0) REVERT: E 95 MET cc_start: 0.9598 (ppp) cc_final: 0.9266 (ppp) REVERT: E 114 GLN cc_start: 0.9658 (OUTLIER) cc_final: 0.9350 (tm-30) REVERT: E 150 MET cc_start: 0.9283 (mpp) cc_final: 0.8885 (mmm) REVERT: E 185 ASN cc_start: 0.8609 (t0) cc_final: 0.8286 (t0) REVERT: E 271 MET cc_start: 0.9109 (mmm) cc_final: 0.8681 (mmp) REVERT: F 584 GLU cc_start: 0.9617 (tt0) cc_final: 0.9170 (pt0) REVERT: F 589 ASP cc_start: 0.9366 (m-30) cc_final: 0.8996 (p0) REVERT: F 626 MET cc_start: 0.8851 (tpp) cc_final: 0.8199 (tpp) REVERT: F 648 GLU cc_start: 0.9407 (pp20) cc_final: 0.9168 (pp20) REVERT: F 657 GLU cc_start: 0.9539 (tm-30) cc_final: 0.9278 (tm-30) REVERT: F 661 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8965 (pp) REVERT: H 18 LEU cc_start: 0.9108 (tp) cc_final: 0.8653 (tp) REVERT: H 47 GLU cc_start: 0.9389 (pm20) cc_final: 0.8802 (mp0) REVERT: H 80 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8651 (tp) REVERT: H 82 MET cc_start: 0.9509 (mpp) cc_final: 0.8865 (mpp) REVERT: H 102 TYR cc_start: 0.9085 (m-80) cc_final: 0.8713 (m-10) REVERT: I 3 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8278 (tm-30) REVERT: I 25 SER cc_start: 0.9111 (OUTLIER) cc_final: 0.8866 (p) REVERT: I 47 GLU cc_start: 0.9088 (pm20) cc_final: 0.8316 (pt0) REVERT: I 80 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8391 (tp) REVERT: I 82 MET cc_start: 0.9428 (mpp) cc_final: 0.8897 (mpp) REVERT: I 95 ASP cc_start: 0.9464 (m-30) cc_final: 0.9037 (m-30) REVERT: I 101 GLN cc_start: 0.9442 (mp10) cc_final: 0.8973 (mp10) REVERT: J 22 CYS cc_start: 0.8494 (t) cc_final: 0.8076 (t) REVERT: J 28 ASP cc_start: 0.9200 (p0) cc_final: 0.8840 (p0) REVERT: J 46 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8443 (pm20) REVERT: J 73 ASN cc_start: 0.8329 (p0) cc_final: 0.8123 (p0) REVERT: J 82 ASP cc_start: 0.9458 (t0) cc_final: 0.9035 (m-30) REVERT: J 82 ASN cc_start: 0.9787 (OUTLIER) cc_final: 0.9026 (t0) REVERT: J 86 ASP cc_start: 0.9468 (m-30) cc_final: 0.9120 (m-30) outliers start: 63 outliers final: 50 residues processed: 262 average time/residue: 0.1287 time to fit residues: 51.4924 Evaluate side-chains 260 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 581 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.035397 restraints weight = 85348.862| |-----------------------------------------------------------------------------| r_work (start): 0.2579 rms_B_bonded: 6.25 r_work: 0.2397 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18106 Z= 0.139 Angle : 0.746 15.068 24717 Z= 0.367 Chirality : 0.045 0.254 2962 Planarity : 0.004 0.054 3042 Dihedral : 6.602 58.226 3849 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.82 % Rotamer: Outliers : 3.38 % Allowed : 32.67 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.19), residues: 2077 helix: 2.10 (0.29), residues: 344 sheet: -0.49 (0.21), residues: 648 loop : -1.43 (0.20), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 585 TYR 0.017 0.001 TYR H 102 PHE 0.018 0.001 PHE F 522 TRP 0.026 0.001 TRP A 427 HIS 0.004 0.001 HIS E 216 Details of bonding type rmsd covalent geometry : bond 0.00337 (17991) covalent geometry : angle 0.72175 (24411) SS BOND : bond 0.00558 ( 39) SS BOND : angle 1.95558 ( 78) hydrogen bonds : bond 0.03423 ( 534) hydrogen bonds : angle 4.13086 ( 1413) link_ALPHA1-3 : bond 0.00705 ( 2) link_ALPHA1-3 : angle 2.47197 ( 6) link_BETA1-4 : bond 0.00337 ( 25) link_BETA1-4 : angle 1.17937 ( 75) link_NAG-ASN : bond 0.00347 ( 49) link_NAG-ASN : angle 2.04433 ( 147) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3507.84 seconds wall clock time: 61 minutes 23.58 seconds (3683.58 seconds total)