Starting phenix.real_space_refine on Sun Jun 15 19:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tnh_41416/06_2025/8tnh_41416.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tnh_41416/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tnh_41416/06_2025/8tnh_41416.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tnh_41416/06_2025/8tnh_41416.map" model { file = "/net/cci-nas-00/data/ceres_data/8tnh_41416/06_2025/8tnh_41416.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tnh_41416/06_2025/8tnh_41416.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.48, per 1000 atoms: 0.65 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: 5.39 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.91 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: 5.86 Time building geometry restraints manager: 6.24 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 505 or resid 601 through 607)) selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.110 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP D 596 HIS 0.003 0.001 HIS J 100C PHE 0.023 0.001 PHE J 98 TYR 0.017 0.001 TYR C 484 ARG 0.007 0.000 ARG A 151 Details of bonding type rmsd link_NAG-ASN : bond 0.00611 ( 49) link_NAG-ASN : angle 4.11761 ( 147) link_BETA1-4 : bond 0.00600 ( 25) link_BETA1-4 : angle 1.51379 ( 75) link_ALPHA1-3 : bond 0.00571 ( 2) link_ALPHA1-3 : angle 2.91189 ( 6) hydrogen bonds : bond 0.12875 ( 534) hydrogen bonds : angle 4.87930 ( 1413) SS BOND : bond 0.00625 ( 39) SS BOND : angle 2.33432 ( 78) covalent geometry : bond 0.00495 (17991) covalent geometry : angle 0.77282 (24411) *********************** 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 : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7559 (t0) cc_final: 0.7012 (t0) REVERT: B 588 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6330 (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: 0.8202 (mp) REVERT: I 79 TYR cc_start: 0.8513 (m-80) cc_final: 0.8123 (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: 0.8018 (m-80) outliers start: 9 outliers final: 2 residues processed: 342 average time/residue: 0.4346 time to fit residues: 215.3179 Evaluate side-chains 205 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 203 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 174 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 0.0270 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.4980 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 293 GLN A 330 HIS A 348 GLN B 651 ASN 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 637 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82BASN J 57 GLN J 82BASN J 108 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.038523 restraints weight = 81850.195| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 6.25 r_work: 0.2465 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18106 Z= 0.140 Angle : 0.741 13.598 24717 Z= 0.365 Chirality : 0.047 0.318 2962 Planarity : 0.004 0.041 3042 Dihedral : 10.165 74.935 3852 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.94 % Favored : 91.91 % Rotamer: Outliers : 4.24 % Allowed : 30.42 % Favored : 65.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 2077 helix: 1.92 (0.29), residues: 337 sheet: -0.87 (0.22), residues: 612 loop : -1.72 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 69 HIS 0.007 0.001 HIS J 100C PHE 0.015 0.001 PHE A 382 TYR 0.014 0.001 TYR H 60 ARG 0.006 0.001 ARG E 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 49) link_NAG-ASN : angle 2.94457 ( 147) link_BETA1-4 : bond 0.00299 ( 25) link_BETA1-4 : angle 1.50222 ( 75) link_ALPHA1-3 : bond 0.01094 ( 2) link_ALPHA1-3 : angle 3.10661 ( 6) hydrogen bonds : bond 0.03823 ( 534) hydrogen bonds : angle 4.42914 ( 1413) SS BOND : bond 0.00802 ( 39) SS BOND : angle 1.96637 ( 78) covalent geometry : bond 0.00321 (17991) covalent geometry : angle 0.69451 (24411) *********************** 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 306 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 227 time to evaluate : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9458 (OUTLIER) cc_final: 0.8855 (m100) REVERT: A 95 MET cc_start: 0.9770 (ptm) cc_final: 0.9534 (ppp) REVERT: A 150 MET cc_start: 0.9305 (mtp) cc_final: 0.9023 (mtp) REVERT: B 543 ASN cc_start: 0.9554 (t0) cc_final: 0.9344 (t0) REVERT: B 574 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8681 (pttm) REVERT: B 589 ASP cc_start: 0.9230 (m-30) cc_final: 0.8792 (p0) REVERT: C 42 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8074 (p) REVERT: C 104 MET cc_start: 0.9486 (ttm) cc_final: 0.9244 (ttt) REVERT: C 185 ASN cc_start: 0.8312 (t0) cc_final: 0.7797 (t0) REVERT: C 323 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9207 (pt) REVERT: C 370 GLU cc_start: 0.9221 (mp0) cc_final: 0.8805 (mp0) REVERT: C 381 GLU cc_start: 0.7925 (mp0) cc_final: 0.7697 (mp0) REVERT: C 427 TRP cc_start: 0.9355 (m100) cc_final: 0.8928 (m100) REVERT: D 530 MET cc_start: 0.9414 (mmm) cc_final: 0.9162 (mmt) REVERT: D 589 ASP cc_start: 0.9356 (m-30) cc_final: 0.8854 (p0) REVERT: D 626 MET cc_start: 0.9006 (tpp) cc_final: 0.8716 (mmm) REVERT: D 648 GLU cc_start: 0.9539 (pp20) cc_final: 0.9332 (pp20) REVERT: E 100 MET cc_start: 0.9416 (mtt) cc_final: 0.9195 (mtt) REVERT: E 104 MET cc_start: 0.9335 (ttp) cc_final: 0.8658 (tmm) REVERT: E 185 ASN cc_start: 0.8006 (t0) cc_final: 0.7779 (t0) REVERT: E 271 MET cc_start: 0.8287 (mmm) cc_final: 0.8039 (mmm) REVERT: E 426 MET cc_start: 0.8799 (ttp) cc_final: 0.8425 (ptt) REVERT: E 427 TRP cc_start: 0.9415 (m100) cc_final: 0.9063 (m100) REVERT: F 584 GLU cc_start: 0.9621 (tt0) cc_final: 0.9089 (pt0) REVERT: F 589 ASP cc_start: 0.9286 (m-30) cc_final: 0.8869 (p0) REVERT: F 626 MET cc_start: 0.8627 (tpp) cc_final: 0.8390 (tpp) REVERT: F 637 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8901 (p0) REVERT: F 648 GLU cc_start: 0.9392 (pp20) cc_final: 0.9059 (pp20) REVERT: F 657 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8989 (tm-30) REVERT: F 661 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9002 (pp) REVERT: H 60 TYR cc_start: 0.9372 (m-80) cc_final: 0.9023 (m-80) REVERT: H 105 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8316 (tm-30) REVERT: I 3 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8406 (tm-30) REVERT: I 18 LEU cc_start: 0.8611 (mt) cc_final: 0.8086 (mp) REVERT: I 60 TYR cc_start: 0.9492 (m-80) cc_final: 0.9188 (m-80) REVERT: I 82 MET cc_start: 0.9541 (mpp) cc_final: 0.8963 (mpp) REVERT: I 82 ASP cc_start: 0.9519 (m-30) cc_final: 0.9230 (p0) REVERT: I 82 ASN cc_start: 0.9706 (OUTLIER) cc_final: 0.9177 (t0) REVERT: I 95 ASP cc_start: 0.9379 (m-30) cc_final: 0.9046 (m-30) REVERT: I 101 GLN cc_start: 0.9235 (mp10) cc_final: 0.8914 (mp10) REVERT: J 3 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8441 (tm-30) REVERT: J 28 ASP cc_start: 0.9143 (p0) cc_final: 0.8846 (p0) REVERT: J 30 GLU cc_start: 0.8680 (mp0) cc_final: 0.8338 (mp0) REVERT: J 86 ASP cc_start: 0.9147 (m-30) cc_final: 0.8828 (m-30) outliers start: 79 outliers final: 26 residues processed: 301 average time/residue: 0.4113 time to fit residues: 183.9118 Evaluate side-chains 233 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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 323 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 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 636 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 ASN 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 180 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 432 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 478 ASN F 591 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.034567 restraints weight = 86273.692| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 6.19 r_work: 0.2344 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.2344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 18106 Z= 0.347 Angle : 0.837 16.166 24717 Z= 0.411 Chirality : 0.047 0.275 2962 Planarity : 0.004 0.042 3042 Dihedral : 9.135 59.560 3851 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.39 % Favored : 90.47 % Rotamer: Outliers : 5.15 % Allowed : 29.67 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 2077 helix: 2.18 (0.29), residues: 337 sheet: -0.81 (0.21), residues: 666 loop : -1.71 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 479 HIS 0.004 0.001 HIS J 100C PHE 0.019 0.002 PHE A 382 TYR 0.017 0.002 TYR H 91 ARG 0.005 0.001 ARG F 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00763 ( 49) link_NAG-ASN : angle 2.96891 ( 147) link_BETA1-4 : bond 0.00337 ( 25) link_BETA1-4 : angle 1.63560 ( 75) link_ALPHA1-3 : bond 0.00985 ( 2) link_ALPHA1-3 : angle 2.73655 ( 6) hydrogen bonds : bond 0.04790 ( 534) hydrogen bonds : angle 4.58993 ( 1413) SS BOND : bond 0.00595 ( 39) SS BOND : angle 2.27357 ( 78) covalent geometry : bond 0.00768 (17991) covalent geometry : angle 0.79314 (24411) *********************** 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 297 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 201 time to evaluate : 3.002 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: 0.9774 (t0) cc_final: 0.9398 (p0) REVERT: A 95 MET cc_start: 0.9765 (ptm) cc_final: 0.9388 (ppp) REVERT: A 104 MET cc_start: 0.9130 (tmm) cc_final: 0.8830 (tmm) REVERT: A 107 ASP cc_start: 0.9508 (t0) cc_final: 0.9159 (m-30) REVERT: A 150 MET cc_start: 0.9335 (mtp) cc_final: 0.8655 (mtp) REVERT: A 271 MET cc_start: 0.8638 (mmm) cc_final: 0.8422 (mmm) REVERT: A 278 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9263 (p) REVERT: B 543 ASN cc_start: 0.9653 (t0) cc_final: 0.9437 (t0) REVERT: B 589 ASP cc_start: 0.9281 (m-30) cc_final: 0.8820 (p0) REVERT: B 605 CYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8165 (t) REVERT: B 626 MET cc_start: 0.8636 (tpp) cc_final: 0.8411 (tpt) REVERT: B 632 ASP cc_start: 0.9773 (t0) cc_final: 0.9255 (p0) REVERT: B 638 TYR cc_start: 0.9381 (m-10) cc_final: 0.9129 (m-10) REVERT: C 185 ASN cc_start: 0.8147 (t0) cc_final: 0.7807 (t0) REVERT: C 323 ILE cc_start: 0.9675 (OUTLIER) cc_final: 0.9125 (pt) REVERT: D 530 MET cc_start: 0.9295 (mmm) cc_final: 0.9060 (mmm) REVERT: D 542 ARG cc_start: 0.9664 (ttp80) cc_final: 0.9376 (ttp-110) REVERT: D 589 ASP cc_start: 0.9317 (m-30) cc_final: 0.8947 (p0) REVERT: E 54 CYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7734 (t) REVERT: E 87 GLU cc_start: 0.9468 (OUTLIER) cc_final: 0.9236 (mp0) REVERT: E 100 MET cc_start: 0.9508 (mtt) cc_final: 0.9208 (mtt) REVERT: E 104 MET cc_start: 0.9495 (ttp) cc_final: 0.9031 (tmm) REVERT: E 107 ASP cc_start: 0.9595 (t0) cc_final: 0.9194 (m-30) REVERT: E 185 ASN cc_start: 0.8278 (t0) cc_final: 0.7959 (t0) REVERT: F 626 MET cc_start: 0.8762 (tpp) cc_final: 0.8450 (tpp) REVERT: F 637 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.8892 (p0) REVERT: F 648 GLU cc_start: 0.9336 (pp20) cc_final: 0.9104 (pp20) REVERT: F 657 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9043 (tm-30) REVERT: F 661 LEU cc_start: 0.9530 (OUTLIER) cc_final: 0.9083 (pp) REVERT: H 80 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8864 (tp) REVERT: H 82 MET cc_start: 0.9343 (mpp) cc_final: 0.8450 (mpp) REVERT: H 82 ASP cc_start: 0.9531 (m-30) cc_final: 0.9197 (p0) REVERT: I 3 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8266 (tm-30) REVERT: I 22 CYS cc_start: 0.8258 (t) cc_final: 0.7882 (t) REVERT: I 25 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8797 (p) REVERT: I 82 MET cc_start: 0.9522 (mpp) cc_final: 0.9097 (mpp) REVERT: J 22 CYS cc_start: 0.8148 (t) cc_final: 0.7797 (t) REVERT: J 44 GLU cc_start: 0.8796 (tp30) cc_final: 0.8590 (tm-30) REVERT: J 86 ASP cc_start: 0.9288 (m-30) cc_final: 0.9035 (m-30) REVERT: J 97 GLN cc_start: 0.9416 (mt0) cc_final: 0.9127 (mp10) outliers start: 96 outliers final: 53 residues processed: 284 average time/residue: 0.4047 time to fit residues: 174.3136 Evaluate side-chains 250 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 2.281 ------------------------------------------------------------------------------- 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 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 54 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 LEU 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 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 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 87 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 120 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 442 VAL 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 637 ASN 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 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 25 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE 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 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 175 optimal weight: 0.0030 overall best weight: 2.3596 ------------------------------------------------------------------------------- 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 = 0.2990 r_free = 0.2990 target = 0.047995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.035223 restraints weight = 84799.734| |-----------------------------------------------------------------------------| r_work (start): 0.2549 rms_B_bonded: 6.24 r_work: 0.2369 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2963 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= 0.182 Angle : 0.720 16.052 24717 Z= 0.357 Chirality : 0.045 0.255 2962 Planarity : 0.004 0.042 3042 Dihedral : 8.234 59.362 3851 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.57 % Favored : 91.38 % Rotamer: Outliers : 4.29 % Allowed : 31.12 % Favored : 64.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.19), residues: 2077 helix: 2.23 (0.29), residues: 337 sheet: -0.75 (0.21), residues: 666 loop : -1.59 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.015 0.001 PHE A 382 TYR 0.012 0.001 TYR E 61 ARG 0.005 0.000 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 49) link_NAG-ASN : angle 2.57364 ( 147) link_BETA1-4 : bond 0.00266 ( 25) link_BETA1-4 : angle 1.38755 ( 75) link_ALPHA1-3 : bond 0.00970 ( 2) link_ALPHA1-3 : angle 2.90347 ( 6) hydrogen bonds : bond 0.04044 ( 534) hydrogen bonds : angle 4.31223 ( 1413) SS BOND : bond 0.00591 ( 39) SS BOND : angle 2.30750 ( 78) covalent geometry : bond 0.00420 (17991) covalent geometry : angle 0.67847 (24411) *********************** 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 288 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 2.712 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 80 ASN cc_start: 0.9776 (t0) cc_final: 0.9362 (p0) REVERT: A 95 MET cc_start: 0.9765 (ptm) cc_final: 0.9366 (ppp) REVERT: A 101 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8883 (m) REVERT: A 104 MET cc_start: 0.9100 (tmm) cc_final: 0.8807 (tmm) REVERT: A 107 ASP cc_start: 0.9522 (t0) cc_final: 0.9176 (m-30) REVERT: A 150 MET cc_start: 0.9288 (mtp) cc_final: 0.8940 (mtp) REVERT: A 185 ASN cc_start: 0.8976 (t0) cc_final: 0.8672 (t0) REVERT: A 271 MET cc_start: 0.8705 (mmm) cc_final: 0.8476 (mmm) REVERT: B 543 ASN cc_start: 0.9649 (t0) cc_final: 0.9387 (t0) REVERT: B 589 ASP cc_start: 0.9302 (m-30) cc_final: 0.8842 (p0) REVERT: B 626 MET cc_start: 0.8590 (tpp) cc_final: 0.8251 (tpp) REVERT: B 632 ASP cc_start: 0.9752 (t0) cc_final: 0.9220 (p0) REVERT: B 638 TYR cc_start: 0.9373 (m-10) cc_final: 0.9083 (m-10) REVERT: B 654 GLU cc_start: 0.9642 (tm-30) cc_final: 0.9296 (pp20) REVERT: C 42 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8547 (p) REVERT: C 69 TRP cc_start: 0.8915 (m-90) cc_final: 0.8329 (m-90) REVERT: C 95 MET cc_start: 0.9562 (ppp) cc_final: 0.9346 (ppp) REVERT: C 100 MET cc_start: 0.9527 (mtm) cc_final: 0.8966 (mtt) REVERT: C 104 MET cc_start: 0.9617 (ttp) cc_final: 0.9212 (ttp) REVERT: C 150 MET cc_start: 0.9517 (mtm) cc_final: 0.9308 (mtm) REVERT: C 185 ASN cc_start: 0.8035 (t0) cc_final: 0.7659 (t0) REVERT: C 278 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9306 (p) REVERT: C 323 ILE cc_start: 0.9683 (OUTLIER) cc_final: 0.9160 (pt) REVERT: C 370 GLU cc_start: 0.9216 (mp0) cc_final: 0.8563 (mp0) REVERT: C 426 MET cc_start: 0.9036 (ttp) cc_final: 0.8629 (ptt) REVERT: C 427 TRP cc_start: 0.9462 (m100) cc_final: 0.9020 (m100) REVERT: D 542 ARG cc_start: 0.9648 (ttp80) cc_final: 0.9323 (ttp-110) REVERT: D 543 ASN cc_start: 0.9427 (m110) cc_final: 0.8947 (t0) REVERT: D 589 ASP cc_start: 0.9327 (m-30) cc_final: 0.8935 (p0) REVERT: E 54 CYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7551 (t) REVERT: E 87 GLU cc_start: 0.9442 (OUTLIER) cc_final: 0.9196 (mp0) REVERT: E 95 MET cc_start: 0.9551 (ppp) cc_final: 0.9319 (ppp) REVERT: E 104 MET cc_start: 0.9482 (ttp) cc_final: 0.8814 (tmm) REVERT: E 107 ASP cc_start: 0.9599 (t0) cc_final: 0.9187 (m-30) REVERT: E 113 ASP cc_start: 0.9681 (t0) cc_final: 0.9430 (m-30) REVERT: E 114 GLN cc_start: 0.9688 (OUTLIER) cc_final: 0.9385 (tm-30) REVERT: E 150 MET cc_start: 0.9530 (tpp) cc_final: 0.9136 (mpp) REVERT: E 185 ASN cc_start: 0.8293 (t0) cc_final: 0.7944 (t0) REVERT: F 584 GLU cc_start: 0.9654 (tt0) cc_final: 0.9154 (pt0) REVERT: F 589 ASP cc_start: 0.9395 (m-30) cc_final: 0.8991 (p0) REVERT: F 626 MET cc_start: 0.8652 (tpp) cc_final: 0.8371 (tpp) REVERT: F 634 GLU cc_start: 0.8907 (tm-30) cc_final: 0.8580 (tm-30) REVERT: F 637 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8890 (p0) REVERT: F 648 GLU cc_start: 0.9346 (pp20) cc_final: 0.9091 (pp20) REVERT: F 657 GLU cc_start: 0.9325 (tm-30) cc_final: 0.9104 (tm-30) REVERT: F 661 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9038 (pp) REVERT: H 18 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8512 (tp) REVERT: H 80 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8894 (tp) REVERT: H 82 MET cc_start: 0.9381 (mpp) cc_final: 0.8705 (mpp) REVERT: I 3 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8414 (tm-30) REVERT: I 74 GLU cc_start: 0.9477 (pp20) cc_final: 0.9253 (pp20) REVERT: I 82 MET cc_start: 0.9580 (mpp) cc_final: 0.9062 (mpp) REVERT: I 101 GLN cc_start: 0.9304 (mp10) cc_final: 0.9015 (mp10) REVERT: J 3 GLN cc_start: 0.8884 (tm-30) cc_final: 0.8628 (tm-30) REVERT: J 22 CYS cc_start: 0.8248 (t) cc_final: 0.7895 (t) REVERT: J 28 ASP cc_start: 0.9226 (p0) cc_final: 0.9022 (p0) REVERT: J 44 GLU cc_start: 0.8822 (tp30) cc_final: 0.8612 (tm-30) REVERT: J 86 ASP cc_start: 0.9362 (m-30) cc_final: 0.9101 (m-30) REVERT: J 97 GLN cc_start: 0.9422 (mt0) cc_final: 0.9156 (mm110) REVERT: J 101 GLN cc_start: 0.9095 (mp10) cc_final: 0.8755 (mp10) outliers start: 80 outliers final: 47 residues processed: 277 average time/residue: 0.3410 time to fit residues: 144.6728 Evaluate side-chains 250 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 192 time to evaluate : 2.208 ------------------------------------------------------------------------------- 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 101 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 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 116 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 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 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 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 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 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 568 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 637 ASN 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 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 110 THR 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 J residue 11 SER 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 132 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 101 optimal weight: 0.4980 chunk 65 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.035206 restraints weight = 85894.188| |-----------------------------------------------------------------------------| r_work (start): 0.2553 rms_B_bonded: 6.24 r_work: 0.2370 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 18106 Z= 0.174 Angle : 0.704 15.093 24717 Z= 0.349 Chirality : 0.045 0.248 2962 Planarity : 0.004 0.042 3042 Dihedral : 7.727 59.604 3849 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.76 % Favored : 91.14 % Rotamer: Outliers : 4.61 % Allowed : 30.26 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.19), residues: 2077 helix: 2.32 (0.29), residues: 327 sheet: -0.70 (0.21), residues: 654 loop : -1.59 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 479 HIS 0.003 0.001 HIS E 216 PHE 0.015 0.001 PHE A 382 TYR 0.017 0.001 TYR A 39 ARG 0.006 0.000 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 49) link_NAG-ASN : angle 2.44340 ( 147) link_BETA1-4 : bond 0.00280 ( 25) link_BETA1-4 : angle 1.34270 ( 75) link_ALPHA1-3 : bond 0.00979 ( 2) link_ALPHA1-3 : angle 2.86217 ( 6) hydrogen bonds : bond 0.03887 ( 534) hydrogen bonds : angle 4.29894 ( 1413) SS BOND : bond 0.00557 ( 39) SS BOND : angle 2.14004 ( 78) covalent geometry : bond 0.00403 (17991) covalent geometry : angle 0.66609 (24411) *********************** 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 289 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 203 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9766 (t0) cc_final: 0.9316 (p0) REVERT: A 95 MET cc_start: 0.9774 (ptm) cc_final: 0.9387 (ppp) REVERT: A 100 MET cc_start: 0.9537 (mtp) cc_final: 0.9323 (mtt) REVERT: A 104 MET cc_start: 0.9124 (tmm) cc_final: 0.8912 (tmm) REVERT: A 114 GLN cc_start: 0.9594 (tm-30) cc_final: 0.9392 (tm-30) REVERT: A 150 MET cc_start: 0.9311 (mtp) cc_final: 0.8941 (mtp) REVERT: A 271 MET cc_start: 0.8767 (mmm) cc_final: 0.8549 (mmm) REVERT: A 278 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9257 (p) REVERT: A 426 MET cc_start: 0.9112 (ttp) cc_final: 0.8912 (ppp) REVERT: B 543 ASN cc_start: 0.9642 (t0) cc_final: 0.9363 (t0) REVERT: B 589 ASP cc_start: 0.9301 (m-30) cc_final: 0.8821 (p0) REVERT: B 605 CYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 626 MET cc_start: 0.8561 (tpp) cc_final: 0.8142 (tpp) REVERT: B 638 TYR cc_start: 0.9372 (m-10) cc_final: 0.9074 (m-10) REVERT: C 42 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8327 (p) REVERT: C 69 TRP cc_start: 0.8962 (m-90) cc_final: 0.8227 (m-90) REVERT: C 95 MET cc_start: 0.9562 (ppp) cc_final: 0.9300 (ppp) REVERT: C 100 MET cc_start: 0.9563 (mtm) cc_final: 0.8964 (mtt) REVERT: C 104 MET cc_start: 0.9606 (ttp) cc_final: 0.9234 (ttp) REVERT: C 150 MET cc_start: 0.9530 (mtm) cc_final: 0.9026 (mtt) REVERT: C 161 MET cc_start: 0.9496 (tpp) cc_final: 0.9282 (tpp) REVERT: C 185 ASN cc_start: 0.8113 (t0) cc_final: 0.7753 (t0) REVERT: C 278 THR cc_start: 0.9577 (OUTLIER) cc_final: 0.9287 (p) REVERT: C 370 GLU cc_start: 0.9227 (mp0) cc_final: 0.8559 (mp0) REVERT: C 381 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8135 (mm-30) REVERT: D 543 ASN cc_start: 0.9424 (m110) cc_final: 0.8977 (t0) REVERT: D 589 ASP cc_start: 0.9347 (m-30) cc_final: 0.8935 (p0) REVERT: E 54 CYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7497 (t) REVERT: E 87 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9224 (mp0) REVERT: E 95 MET cc_start: 0.9573 (ppp) cc_final: 0.9299 (ppp) REVERT: E 100 MET cc_start: 0.9679 (mtp) cc_final: 0.9397 (mtt) REVERT: E 104 MET cc_start: 0.9469 (ttp) cc_final: 0.8918 (tmm) REVERT: E 107 ASP cc_start: 0.9625 (t0) cc_final: 0.9187 (m-30) REVERT: E 150 MET cc_start: 0.9538 (tpp) cc_final: 0.9047 (mpp) REVERT: E 185 ASN cc_start: 0.8374 (t0) cc_final: 0.8023 (t0) REVERT: F 519 PHE cc_start: 0.8120 (t80) cc_final: 0.7798 (t80) REVERT: F 530 MET cc_start: 0.9206 (mmm) cc_final: 0.8978 (mmm) REVERT: F 584 GLU cc_start: 0.9652 (tt0) cc_final: 0.9148 (pt0) REVERT: F 589 ASP cc_start: 0.9382 (m-30) cc_final: 0.9008 (p0) REVERT: F 634 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8599 (tm-30) REVERT: F 648 GLU cc_start: 0.9389 (pp20) cc_final: 0.9144 (pp20) REVERT: F 661 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.8978 (pp) REVERT: H 18 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8533 (tp) REVERT: H 80 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8873 (tp) REVERT: H 82 MET cc_start: 0.9440 (mpp) cc_final: 0.8783 (mpp) REVERT: I 3 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8258 (tm-30) REVERT: I 25 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (p) REVERT: I 28 ASP cc_start: 0.9065 (p0) cc_final: 0.8819 (p0) REVERT: I 30 GLU cc_start: 0.9021 (pm20) cc_final: 0.8811 (mp0) REVERT: I 74 GLU cc_start: 0.9463 (pp20) cc_final: 0.9259 (pp20) REVERT: I 82 MET cc_start: 0.9541 (mpp) cc_final: 0.8980 (mpp) REVERT: I 101 GLN cc_start: 0.9298 (mp10) cc_final: 0.8973 (mp10) REVERT: J 22 CYS cc_start: 0.8445 (t) cc_final: 0.8071 (t) REVERT: J 86 ASP cc_start: 0.9403 (m-30) cc_final: 0.9087 (m-30) REVERT: J 97 GLN cc_start: 0.9424 (mt0) cc_final: 0.9164 (mm110) outliers start: 86 outliers final: 51 residues processed: 279 average time/residue: 0.3241 time to fit residues: 137.8139 Evaluate side-chains 256 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 195 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 601 LYS 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 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 247 CYS Chi-restraints excluded: chain C residue 278 THR 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 C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 642 ILE 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 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 274 SER 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 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 100 LEU Chi-restraints excluded: chain I residue 18 LEU 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 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 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 141 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 204 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.034448 restraints weight = 85584.431| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 6.24 r_work: 0.2354 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 18106 Z= 0.209 Angle : 0.714 13.650 24717 Z= 0.355 Chirality : 0.045 0.244 2962 Planarity : 0.004 0.051 3042 Dihedral : 7.429 58.348 3849 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.39 % Favored : 90.52 % Rotamer: Outliers : 5.10 % Allowed : 29.61 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 2077 helix: 2.24 (0.29), residues: 329 sheet: -0.70 (0.21), residues: 666 loop : -1.53 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.015 0.001 PHE A 382 TYR 0.015 0.001 TYR A 39 ARG 0.007 0.000 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 49) link_NAG-ASN : angle 2.40175 ( 147) link_BETA1-4 : bond 0.00233 ( 25) link_BETA1-4 : angle 1.34126 ( 75) link_ALPHA1-3 : bond 0.00884 ( 2) link_ALPHA1-3 : angle 2.76953 ( 6) hydrogen bonds : bond 0.03985 ( 534) hydrogen bonds : angle 4.31847 ( 1413) SS BOND : bond 0.00667 ( 39) SS BOND : angle 2.16309 ( 78) covalent geometry : bond 0.00477 (17991) covalent geometry : angle 0.67707 (24411) *********************** 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 294 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 199 time to evaluate : 6.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8445 (OUTLIER) cc_final: 0.8219 (p) REVERT: A 95 MET cc_start: 0.9767 (ptm) cc_final: 0.9391 (ppp) REVERT: A 104 MET cc_start: 0.9213 (tmm) cc_final: 0.8963 (tmm) REVERT: A 150 MET cc_start: 0.9324 (mtp) cc_final: 0.8956 (mtp) REVERT: A 271 MET cc_start: 0.8805 (mmm) cc_final: 0.8573 (mmm) REVERT: A 278 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9237 (p) REVERT: B 543 ASN cc_start: 0.9653 (t0) cc_final: 0.9372 (t0) REVERT: B 605 CYS cc_start: 0.9017 (OUTLIER) cc_final: 0.8101 (t) REVERT: B 626 MET cc_start: 0.8580 (tpp) cc_final: 0.8180 (tpp) REVERT: B 638 TYR cc_start: 0.9366 (m-10) cc_final: 0.9011 (m-10) REVERT: B 654 GLU cc_start: 0.9600 (tm-30) cc_final: 0.9246 (pp20) REVERT: B 655 LYS cc_start: 0.9427 (ptpt) cc_final: 0.9169 (pttm) REVERT: C 42 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8501 (p) REVERT: C 69 TRP cc_start: 0.9007 (m-90) cc_final: 0.8148 (m-90) REVERT: C 95 MET cc_start: 0.9578 (ppp) cc_final: 0.9303 (ppp) REVERT: C 104 MET cc_start: 0.9632 (ttp) cc_final: 0.9273 (ttp) REVERT: C 185 ASN cc_start: 0.8179 (t0) cc_final: 0.7826 (t0) REVERT: C 278 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9284 (p) REVERT: C 364 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7739 (t) REVERT: C 370 GLU cc_start: 0.9234 (mp0) cc_final: 0.8537 (mp0) REVERT: C 381 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8160 (mm-30) REVERT: D 543 ASN cc_start: 0.9443 (m110) cc_final: 0.8933 (t0) REVERT: D 589 ASP cc_start: 0.9381 (m-30) cc_final: 0.8951 (p0) REVERT: E 54 CYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7252 (t) REVERT: E 95 MET cc_start: 0.9587 (ppp) cc_final: 0.9295 (ppp) REVERT: E 100 MET cc_start: 0.9569 (mtp) cc_final: 0.9333 (mtt) REVERT: E 104 MET cc_start: 0.9466 (ttp) cc_final: 0.8932 (tmm) REVERT: E 107 ASP cc_start: 0.9601 (t0) cc_final: 0.9201 (m-30) REVERT: E 114 GLN cc_start: 0.9664 (OUTLIER) cc_final: 0.9364 (tm-30) REVERT: E 150 MET cc_start: 0.9575 (tpp) cc_final: 0.9125 (mpp) REVERT: E 185 ASN cc_start: 0.8563 (t0) cc_final: 0.8215 (t0) REVERT: E 231 LYS cc_start: 0.9775 (OUTLIER) cc_final: 0.9536 (mmtm) REVERT: E 271 MET cc_start: 0.9160 (mmm) cc_final: 0.8716 (mmp) REVERT: F 584 GLU cc_start: 0.9677 (tt0) cc_final: 0.9206 (pt0) REVERT: F 589 ASP cc_start: 0.9381 (m-30) cc_final: 0.8948 (p0) REVERT: F 626 MET cc_start: 0.8986 (tpp) cc_final: 0.8517 (tpp) REVERT: F 634 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8623 (tm-30) REVERT: F 648 GLU cc_start: 0.9403 (pp20) cc_final: 0.9163 (pp20) REVERT: F 654 GLU cc_start: 0.9580 (tm-30) cc_final: 0.9352 (pp20) REVERT: F 661 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9063 (pp) REVERT: H 18 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8524 (tp) REVERT: H 80 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8777 (tp) REVERT: H 82 MET cc_start: 0.9472 (mpp) cc_final: 0.8746 (mpp) REVERT: I 3 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8252 (tm-30) REVERT: I 25 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (p) REVERT: I 28 ASP cc_start: 0.9100 (p0) cc_final: 0.8861 (p0) REVERT: I 29 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9309 (m) REVERT: I 74 GLU cc_start: 0.9478 (pp20) cc_final: 0.9240 (pp20) REVERT: I 80 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8466 (tp) REVERT: I 82 MET cc_start: 0.9502 (mpp) cc_final: 0.8964 (mpp) REVERT: J 3 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8431 (tm-30) REVERT: J 22 CYS cc_start: 0.8456 (t) cc_final: 0.8062 (t) REVERT: J 86 ASP cc_start: 0.9460 (m-30) cc_final: 0.9172 (m-30) REVERT: J 97 GLN cc_start: 0.9437 (mt0) cc_final: 0.9176 (mm110) outliers start: 95 outliers final: 60 residues processed: 281 average time/residue: 0.3845 time to fit residues: 167.6590 Evaluate side-chains 268 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 193 time to evaluate : 3.370 ------------------------------------------------------------------------------- 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 465 THR Chi-restraints excluded: chain B residue 601 LYS 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 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 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 278 THR 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 364 SER 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 603 ILE Chi-restraints excluded: chain D residue 604 CYS 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 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 465 THR Chi-restraints excluded: chain F residue 568 LEU 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 46 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 175 optimal weight: 0.0470 chunk 173 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 196 optimal weight: 20.0000 chunk 140 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 159 optimal weight: 0.0170 chunk 71 optimal weight: 3.9990 overall best weight: 2.6122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2975 r_free = 0.2975 target = 0.047166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.034663 restraints weight = 85480.021| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 6.19 r_work: 0.2363 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 18106 Z= 0.189 Angle : 0.719 13.300 24717 Z= 0.359 Chirality : 0.045 0.241 2962 Planarity : 0.004 0.052 3042 Dihedral : 7.142 58.294 3849 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.96 % Favored : 90.95 % Rotamer: Outliers : 4.67 % Allowed : 30.47 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.19), residues: 2077 helix: 2.24 (0.29), residues: 329 sheet: -0.61 (0.21), residues: 654 loop : -1.52 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.031 0.001 PHE F 519 TYR 0.013 0.001 TYR A 39 ARG 0.007 0.000 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 49) link_NAG-ASN : angle 2.20064 ( 147) link_BETA1-4 : bond 0.00272 ( 25) link_BETA1-4 : angle 1.29025 ( 75) link_ALPHA1-3 : bond 0.00811 ( 2) link_ALPHA1-3 : angle 2.68654 ( 6) hydrogen bonds : bond 0.03884 ( 534) hydrogen bonds : angle 4.27650 ( 1413) SS BOND : bond 0.00609 ( 39) SS BOND : angle 2.08734 ( 78) covalent geometry : bond 0.00438 (17991) covalent geometry : angle 0.68861 (24411) *********************** 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 285 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 3.490 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: 0.8466 (OUTLIER) cc_final: 0.8222 (p) REVERT: A 80 ASN cc_start: 0.9742 (t0) cc_final: 0.9271 (p0) REVERT: A 95 MET cc_start: 0.9766 (ptm) cc_final: 0.9397 (ppp) REVERT: A 104 MET cc_start: 0.9225 (tmm) cc_final: 0.8928 (tmm) REVERT: A 150 MET cc_start: 0.9321 (mtp) cc_final: 0.9114 (mtp) REVERT: A 271 MET cc_start: 0.8823 (mmm) cc_final: 0.8578 (mmm) REVERT: B 543 ASN cc_start: 0.9656 (t0) cc_final: 0.9404 (t0) REVERT: B 605 CYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8142 (t) REVERT: B 626 MET cc_start: 0.8572 (tpp) cc_final: 0.8147 (tpp) REVERT: B 638 TYR cc_start: 0.9372 (m-10) cc_final: 0.8990 (m-10) REVERT: B 654 GLU cc_start: 0.9574 (OUTLIER) cc_final: 0.9216 (pp20) REVERT: B 655 LYS cc_start: 0.9430 (ptpt) cc_final: 0.9160 (pttm) REVERT: C 42 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8481 (p) REVERT: C 69 TRP cc_start: 0.9005 (m-90) cc_final: 0.7995 (m-90) REVERT: C 95 MET cc_start: 0.9583 (ppp) cc_final: 0.9288 (ppp) REVERT: C 100 MET cc_start: 0.9563 (mtm) cc_final: 0.8987 (mtt) REVERT: C 104 MET cc_start: 0.9631 (ttp) cc_final: 0.9287 (ttp) REVERT: C 185 ASN cc_start: 0.8225 (t0) cc_final: 0.7874 (t0) REVERT: C 278 THR cc_start: 0.9579 (OUTLIER) cc_final: 0.9292 (p) REVERT: C 364 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7709 (t) REVERT: C 370 GLU cc_start: 0.9228 (mp0) cc_final: 0.8633 (mp0) REVERT: C 381 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8144 (mm-30) REVERT: D 543 ASN cc_start: 0.9435 (m110) cc_final: 0.8909 (t0) REVERT: D 584 GLU cc_start: 0.9718 (tt0) cc_final: 0.9261 (tm-30) REVERT: D 589 ASP cc_start: 0.9383 (m-30) cc_final: 0.8948 (p0) REVERT: D 626 MET cc_start: 0.8832 (tpp) cc_final: 0.8546 (tpp) REVERT: E 54 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7392 (t) REVERT: E 87 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9238 (mp0) REVERT: E 95 MET cc_start: 0.9600 (ppp) cc_final: 0.9293 (ppp) REVERT: E 100 MET cc_start: 0.9576 (mtp) cc_final: 0.9340 (mtt) REVERT: E 104 MET cc_start: 0.9441 (ttp) cc_final: 0.8948 (tmm) REVERT: E 114 GLN cc_start: 0.9668 (OUTLIER) cc_final: 0.9367 (tm-30) REVERT: E 150 MET cc_start: 0.9594 (OUTLIER) cc_final: 0.9197 (mpp) REVERT: E 185 ASN cc_start: 0.8553 (t0) cc_final: 0.8204 (t0) REVERT: F 584 GLU cc_start: 0.9671 (tt0) cc_final: 0.9239 (pt0) REVERT: F 589 ASP cc_start: 0.9398 (m-30) cc_final: 0.9037 (p0) REVERT: F 634 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8688 (tm-30) REVERT: F 648 GLU cc_start: 0.9413 (pp20) cc_final: 0.9167 (pp20) REVERT: F 661 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9104 (pp) REVERT: H 18 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8566 (tp) REVERT: H 80 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8773 (tp) REVERT: H 82 MET cc_start: 0.9475 (mpp) cc_final: 0.8786 (mpp) REVERT: I 3 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8244 (tm-30) REVERT: I 25 SER cc_start: 0.9091 (OUTLIER) cc_final: 0.8830 (p) REVERT: I 80 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8478 (tp) REVERT: I 82 MET cc_start: 0.9476 (mpp) cc_final: 0.8908 (mpp) REVERT: J 22 CYS cc_start: 0.8539 (t) cc_final: 0.8169 (t) REVERT: J 46 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8476 (pm20) REVERT: J 82 ASP cc_start: 0.9426 (t0) cc_final: 0.9185 (m-30) REVERT: J 86 ASP cc_start: 0.9526 (m-30) cc_final: 0.9203 (m-30) REVERT: J 97 GLN cc_start: 0.9448 (mt0) cc_final: 0.9195 (mm110) outliers start: 87 outliers final: 61 residues processed: 272 average time/residue: 0.4245 time to fit residues: 177.5165 Evaluate side-chains 269 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 193 time to evaluate : 4.799 ------------------------------------------------------------------------------- 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 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 654 GLU 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 125 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 278 THR 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 364 SER 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 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 642 ILE 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 150 MET 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 568 LEU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 139 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2952 r_free = 0.2952 target = 0.046407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.033881 restraints weight = 86837.263| |-----------------------------------------------------------------------------| r_work (start): 0.2523 rms_B_bonded: 6.22 r_work: 0.2337 rms_B_bonded: 6.12 restraints_weight: 2.0000 r_work (final): 0.2337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3714 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= 0.245 Angle : 0.761 13.045 24717 Z= 0.377 Chirality : 0.045 0.239 2962 Planarity : 0.004 0.053 3042 Dihedral : 7.057 58.102 3849 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.68 % Favored : 90.23 % Rotamer: Outliers : 4.99 % Allowed : 30.15 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.19), residues: 2077 helix: 2.55 (0.29), residues: 309 sheet: -0.64 (0.21), residues: 666 loop : -1.46 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.015 0.001 PHE A 382 TYR 0.015 0.002 TYR J 102 ARG 0.007 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 49) link_NAG-ASN : angle 2.27459 ( 147) link_BETA1-4 : bond 0.00191 ( 25) link_BETA1-4 : angle 1.35133 ( 75) link_ALPHA1-3 : bond 0.00870 ( 2) link_ALPHA1-3 : angle 2.64087 ( 6) hydrogen bonds : bond 0.04143 ( 534) hydrogen bonds : angle 4.37151 ( 1413) SS BOND : bond 0.00764 ( 39) SS BOND : angle 2.12655 ( 78) covalent geometry : bond 0.00554 (17991) covalent geometry : angle 0.73063 (24411) *********************** 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 291 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 198 time to evaluate : 1.978 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 42 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 95 MET cc_start: 0.9746 (ptm) cc_final: 0.9379 (ppp) REVERT: A 104 MET cc_start: 0.9295 (tmm) cc_final: 0.8948 (tmm) REVERT: A 150 MET cc_start: 0.9355 (mtp) cc_final: 0.9146 (mtp) REVERT: A 271 MET cc_start: 0.8910 (mmm) cc_final: 0.8656 (mmm) REVERT: A 278 THR cc_start: 0.9482 (OUTLIER) cc_final: 0.9190 (p) REVERT: B 543 ASN cc_start: 0.9675 (t0) cc_final: 0.9430 (t0) REVERT: B 584 GLU cc_start: 0.9649 (tt0) cc_final: 0.9207 (tm-30) REVERT: B 605 CYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8201 (t) REVERT: B 626 MET cc_start: 0.8678 (tpp) cc_final: 0.8253 (tpp) REVERT: B 638 TYR cc_start: 0.9405 (m-10) cc_final: 0.9026 (m-10) REVERT: B 654 GLU cc_start: 0.9562 (OUTLIER) cc_final: 0.9209 (pp20) REVERT: B 655 LYS cc_start: 0.9428 (ptpt) cc_final: 0.9132 (pttm) REVERT: C 42 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8632 (p) REVERT: C 95 MET cc_start: 0.9582 (ppp) cc_final: 0.9280 (ppp) REVERT: C 100 MET cc_start: 0.9592 (mtm) cc_final: 0.9018 (mtt) REVERT: C 104 MET cc_start: 0.9654 (ttp) cc_final: 0.9280 (ttp) REVERT: C 185 ASN cc_start: 0.8356 (t0) cc_final: 0.8013 (t0) REVERT: C 364 SER cc_start: 0.8203 (OUTLIER) cc_final: 0.7811 (t) REVERT: C 370 GLU cc_start: 0.9257 (mp0) cc_final: 0.8668 (mp0) REVERT: C 381 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 543 ASN cc_start: 0.9442 (m110) cc_final: 0.8962 (t0) REVERT: D 589 ASP cc_start: 0.9386 (m-30) cc_final: 0.8962 (p0) REVERT: D 626 MET cc_start: 0.9031 (tpp) cc_final: 0.8659 (tpp) REVERT: D 654 GLU cc_start: 0.9394 (pp20) cc_final: 0.9024 (pp20) REVERT: E 54 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7535 (t) REVERT: E 100 MET cc_start: 0.9579 (mtp) cc_final: 0.9329 (mtt) REVERT: E 104 MET cc_start: 0.9474 (ttp) cc_final: 0.9035 (tmm) REVERT: E 107 ASP cc_start: 0.9635 (t0) cc_final: 0.9213 (m-30) REVERT: E 150 MET cc_start: 0.9610 (OUTLIER) cc_final: 0.9322 (mpp) REVERT: E 185 ASN cc_start: 0.8622 (t0) cc_final: 0.8274 (t0) REVERT: E 271 MET cc_start: 0.9184 (mmm) cc_final: 0.8718 (mmp) REVERT: F 584 GLU cc_start: 0.9687 (tt0) cc_final: 0.9289 (pt0) REVERT: F 585 ARG cc_start: 0.9523 (mtp-110) cc_final: 0.9315 (ttm110) REVERT: F 589 ASP cc_start: 0.9398 (m-30) cc_final: 0.9001 (p0) REVERT: F 626 MET cc_start: 0.8999 (tpp) cc_final: 0.8464 (tpp) REVERT: F 634 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8670 (tm-30) REVERT: F 648 GLU cc_start: 0.9428 (pp20) cc_final: 0.9199 (pp20) REVERT: F 657 GLU cc_start: 0.9562 (tm-30) cc_final: 0.9162 (pp20) REVERT: F 661 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9269 (pp) REVERT: H 18 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8604 (tp) REVERT: H 47 GLU cc_start: 0.9140 (pm20) cc_final: 0.8565 (mt-10) REVERT: H 80 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8779 (tp) REVERT: H 82 MET cc_start: 0.9499 (mpp) cc_final: 0.8799 (mpp) REVERT: I 3 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8045 (tm-30) REVERT: I 22 CYS cc_start: 0.8260 (t) cc_final: 0.7871 (t) REVERT: I 25 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8708 (p) REVERT: I 80 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8573 (tp) REVERT: I 82 MET cc_start: 0.9453 (mpp) cc_final: 0.8522 (mpp) REVERT: J 3 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8411 (tm-30) REVERT: J 22 CYS cc_start: 0.8393 (t) cc_final: 0.8023 (t) REVERT: J 82 ASP cc_start: 0.9465 (t0) cc_final: 0.9230 (m-30) REVERT: J 86 ASP cc_start: 0.9528 (m-30) cc_final: 0.9204 (m-30) REVERT: J 97 GLN cc_start: 0.9460 (mt0) cc_final: 0.9226 (mm110) outliers start: 93 outliers final: 67 residues processed: 276 average time/residue: 0.4267 time to fit residues: 179.1883 Evaluate side-chains 272 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 192 time to evaluate : 2.790 ------------------------------------------------------------------------------- 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 110 SER 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 446 VAL Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 654 GLU 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 125 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 364 SER 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 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 150 MET 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 442 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 568 LEU 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 46 GLU 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 94 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 82 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 151 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2968 r_free = 0.2968 target = 0.046783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.034562 restraints weight = 87354.569| |-----------------------------------------------------------------------------| r_work (start): 0.2544 rms_B_bonded: 6.18 r_work: 0.2361 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3794 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= 0.178 Angle : 0.744 13.122 24717 Z= 0.372 Chirality : 0.045 0.246 2962 Planarity : 0.004 0.057 3042 Dihedral : 6.880 58.516 3849 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.71 % Favored : 91.19 % Rotamer: Outliers : 4.40 % Allowed : 30.74 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 2077 helix: 2.51 (0.29), residues: 311 sheet: -0.56 (0.21), residues: 654 loop : -1.43 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.027 0.001 PHE F 519 TYR 0.032 0.001 TYR J 102 ARG 0.008 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 49) link_NAG-ASN : angle 2.15294 ( 147) link_BETA1-4 : bond 0.00267 ( 25) link_BETA1-4 : angle 1.25225 ( 75) link_ALPHA1-3 : bond 0.00853 ( 2) link_ALPHA1-3 : angle 2.59572 ( 6) hydrogen bonds : bond 0.03878 ( 534) hydrogen bonds : angle 4.28447 ( 1413) SS BOND : bond 0.00554 ( 39) SS BOND : angle 2.12873 ( 78) covalent geometry : bond 0.00418 (17991) covalent geometry : angle 0.71533 (24411) *********************** 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 284 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 202 time to evaluate : 6.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8246 (p) REVERT: A 95 MET cc_start: 0.9769 (ptm) cc_final: 0.9405 (ppp) REVERT: A 104 MET cc_start: 0.9278 (tmm) cc_final: 0.8936 (tmm) REVERT: A 110 SER cc_start: 0.9709 (OUTLIER) cc_final: 0.9494 (p) REVERT: A 150 MET cc_start: 0.9341 (mtp) cc_final: 0.9116 (mtp) REVERT: A 271 MET cc_start: 0.8864 (mmm) cc_final: 0.8603 (mmm) REVERT: A 278 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9182 (p) REVERT: B 543 ASN cc_start: 0.9670 (t0) cc_final: 0.9440 (t0) REVERT: B 584 GLU cc_start: 0.9657 (tt0) cc_final: 0.9203 (tm-30) REVERT: B 605 CYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8137 (t) REVERT: B 626 MET cc_start: 0.8621 (tpp) cc_final: 0.8192 (tpp) REVERT: B 638 TYR cc_start: 0.9392 (m-10) cc_final: 0.8910 (m-10) REVERT: B 654 GLU cc_start: 0.9553 (OUTLIER) cc_final: 0.9214 (pp20) REVERT: B 655 LYS cc_start: 0.9423 (ptpt) cc_final: 0.9170 (pttm) REVERT: C 42 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8543 (p) REVERT: C 69 TRP cc_start: 0.9144 (m-90) cc_final: 0.8024 (m-90) REVERT: C 95 MET cc_start: 0.9601 (ppp) cc_final: 0.9291 (ppp) REVERT: C 100 MET cc_start: 0.9585 (mtm) cc_final: 0.9006 (mtt) REVERT: C 104 MET cc_start: 0.9636 (ttp) cc_final: 0.9386 (ttp) REVERT: C 185 ASN cc_start: 0.8343 (t0) cc_final: 0.7984 (t0) REVERT: C 217 TYR cc_start: 0.8770 (m-80) cc_final: 0.8222 (m-80) REVERT: C 278 THR cc_start: 0.9624 (OUTLIER) cc_final: 0.9381 (p) REVERT: C 364 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7645 (t) REVERT: C 370 GLU cc_start: 0.9229 (mp0) cc_final: 0.8631 (mp0) REVERT: C 381 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8148 (mm-30) REVERT: D 543 ASN cc_start: 0.9422 (m110) cc_final: 0.8954 (t0) REVERT: D 589 ASP cc_start: 0.9394 (m-30) cc_final: 0.8949 (p0) REVERT: D 626 MET cc_start: 0.9073 (tpp) cc_final: 0.8310 (tpt) REVERT: D 654 GLU cc_start: 0.9395 (pp20) cc_final: 0.9034 (pp20) REVERT: E 54 CYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7444 (t) REVERT: E 100 MET cc_start: 0.9572 (mtp) cc_final: 0.9336 (mtt) REVERT: E 104 MET cc_start: 0.9466 (ttp) cc_final: 0.8954 (tmm) REVERT: E 107 ASP cc_start: 0.9637 (t0) cc_final: 0.9220 (m-30) REVERT: E 150 MET cc_start: 0.9618 (OUTLIER) cc_final: 0.9353 (mpp) REVERT: E 185 ASN cc_start: 0.8584 (t0) cc_final: 0.8227 (t0) REVERT: E 271 MET cc_start: 0.9185 (mmm) cc_final: 0.8727 (mmp) REVERT: F 584 GLU cc_start: 0.9674 (tt0) cc_final: 0.9258 (pt0) REVERT: F 585 ARG cc_start: 0.9517 (mtp-110) cc_final: 0.9294 (ttm110) REVERT: F 589 ASP cc_start: 0.9402 (m-30) cc_final: 0.8999 (p0) REVERT: F 626 MET cc_start: 0.9018 (tpp) cc_final: 0.8439 (tpp) REVERT: F 634 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 657 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9149 (pp20) REVERT: F 661 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9254 (pp) REVERT: H 18 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8611 (tp) REVERT: H 80 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8812 (tp) REVERT: H 82 MET cc_start: 0.9520 (mpp) cc_final: 0.8839 (mpp) REVERT: I 3 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8262 (tm-30) REVERT: I 25 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8897 (p) REVERT: I 80 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8529 (tp) REVERT: I 82 MET cc_start: 0.9453 (mpp) cc_final: 0.8520 (mpp) REVERT: J 3 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8393 (tm-30) REVERT: J 22 CYS cc_start: 0.8561 (t) cc_final: 0.8199 (t) REVERT: J 73 ASN cc_start: 0.8337 (p0) cc_final: 0.8128 (p0) REVERT: J 82 ASP cc_start: 0.9455 (t0) cc_final: 0.9185 (m-30) REVERT: J 86 ASP cc_start: 0.9541 (m-30) cc_final: 0.9205 (m-30) REVERT: J 97 GLN cc_start: 0.9466 (mt0) cc_final: 0.9240 (mm110) outliers start: 82 outliers final: 57 residues processed: 269 average time/residue: 0.3108 time to fit residues: 129.1144 Evaluate side-chains 265 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 193 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 110 SER 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 601 LYS Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 654 GLU 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 125 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 213 ILE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 278 THR 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 364 SER 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 D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS 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 135 THR Chi-restraints excluded: chain E residue 150 MET 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 442 VAL Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 661 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 46 GLU 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 94 THR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 64 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 198 optimal weight: 0.0030 chunk 177 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.2996 r_free = 0.2996 target = 0.047864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.035562 restraints weight = 84810.740| |-----------------------------------------------------------------------------| r_work (start): 0.2584 rms_B_bonded: 6.18 r_work: 0.2402 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 18106 Z= 0.130 Angle : 0.747 13.693 24717 Z= 0.372 Chirality : 0.046 0.273 2962 Planarity : 0.004 0.054 3042 Dihedral : 6.631 58.571 3849 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.43 % Favored : 91.48 % Rotamer: Outliers : 2.79 % Allowed : 32.56 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 2077 helix: 2.48 (0.29), residues: 311 sheet: -0.47 (0.21), residues: 654 loop : -1.38 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 479 HIS 0.004 0.001 HIS E 216 PHE 0.012 0.001 PHE A 382 TYR 0.051 0.001 TYR J 102 ARG 0.009 0.001 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 49) link_NAG-ASN : angle 2.03574 ( 147) link_BETA1-4 : bond 0.00405 ( 25) link_BETA1-4 : angle 1.16133 ( 75) link_ALPHA1-3 : bond 0.00771 ( 2) link_ALPHA1-3 : angle 2.56517 ( 6) hydrogen bonds : bond 0.03390 ( 534) hydrogen bonds : angle 4.14232 ( 1413) SS BOND : bond 0.00572 ( 39) SS BOND : angle 2.04693 ( 78) covalent geometry : bond 0.00314 (17991) covalent geometry : angle 0.72148 (24411) ********************** 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: 52 poor density : 215 time to evaluate : 2.371 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 42 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 95 MET cc_start: 0.9753 (ptm) cc_final: 0.9388 (ppp) REVERT: A 104 MET cc_start: 0.9252 (tmm) cc_final: 0.8914 (tmm) REVERT: A 150 MET cc_start: 0.9317 (mtp) cc_final: 0.9095 (mtp) REVERT: A 271 MET cc_start: 0.8777 (mmm) cc_final: 0.8511 (mmm) REVERT: A 278 THR cc_start: 0.9397 (OUTLIER) cc_final: 0.9105 (p) REVERT: B 543 ASN cc_start: 0.9629 (t0) cc_final: 0.9350 (t0) REVERT: B 584 GLU cc_start: 0.9662 (tt0) cc_final: 0.9183 (tm-30) REVERT: B 626 MET cc_start: 0.8501 (tpp) cc_final: 0.8297 (tpt) REVERT: B 638 TYR cc_start: 0.9342 (m-10) cc_final: 0.8828 (m-10) REVERT: B 654 GLU cc_start: 0.9536 (OUTLIER) cc_final: 0.9212 (pp20) REVERT: C 42 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8332 (p) REVERT: C 69 TRP cc_start: 0.9158 (m-90) cc_final: 0.8165 (m-90) REVERT: C 95 MET cc_start: 0.9616 (ppp) cc_final: 0.9308 (ppp) REVERT: C 100 MET cc_start: 0.9576 (mtm) cc_final: 0.8964 (mtt) REVERT: C 104 MET cc_start: 0.9607 (ttp) cc_final: 0.9346 (tmm) REVERT: C 185 ASN cc_start: 0.8271 (t0) cc_final: 0.7973 (t0) REVERT: C 217 TYR cc_start: 0.8634 (m-80) cc_final: 0.8185 (m-80) REVERT: C 278 THR cc_start: 0.9630 (OUTLIER) cc_final: 0.9391 (p) REVERT: C 370 GLU cc_start: 0.9188 (mp0) cc_final: 0.8597 (mp0) REVERT: C 381 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8077 (mm-30) REVERT: D 543 ASN cc_start: 0.9402 (m110) cc_final: 0.8962 (t0) REVERT: D 626 MET cc_start: 0.8985 (tpp) cc_final: 0.8684 (tpp) REVERT: D 654 GLU cc_start: 0.9372 (pp20) cc_final: 0.8975 (pp20) REVERT: E 54 CYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6939 (t) REVERT: E 100 MET cc_start: 0.9568 (mtp) cc_final: 0.9330 (mtt) REVERT: E 104 MET cc_start: 0.9399 (ttp) cc_final: 0.9004 (tmm) REVERT: E 107 ASP cc_start: 0.9598 (t0) cc_final: 0.9162 (m-30) REVERT: E 114 GLN cc_start: 0.9656 (OUTLIER) cc_final: 0.9356 (tm-30) REVERT: E 150 MET cc_start: 0.9656 (OUTLIER) cc_final: 0.9373 (mpp) REVERT: E 185 ASN cc_start: 0.8569 (t0) cc_final: 0.8240 (t0) REVERT: E 271 MET cc_start: 0.9121 (mmm) cc_final: 0.8657 (mmp) REVERT: F 584 GLU cc_start: 0.9669 (tt0) cc_final: 0.9202 (pt0) REVERT: F 589 ASP cc_start: 0.9387 (m-30) cc_final: 0.8988 (p0) REVERT: F 626 MET cc_start: 0.8933 (tpp) cc_final: 0.8283 (tpp) REVERT: F 634 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 657 GLU cc_start: 0.9545 (tm-30) cc_final: 0.9119 (pp20) REVERT: F 661 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9233 (pp) REVERT: H 18 LEU cc_start: 0.9111 (tp) cc_final: 0.8615 (tp) REVERT: H 28 ASP cc_start: 0.9299 (p0) cc_final: 0.8886 (p0) REVERT: H 47 GLU cc_start: 0.9143 (pm20) cc_final: 0.8563 (mt-10) REVERT: H 80 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8657 (tp) REVERT: H 82 MET cc_start: 0.9525 (mpp) cc_final: 0.8812 (mpp) REVERT: H 102 TYR cc_start: 0.9201 (m-80) cc_final: 0.8866 (m-10) REVERT: I 3 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8260 (tm-30) REVERT: I 25 SER cc_start: 0.9093 (OUTLIER) cc_final: 0.8848 (p) REVERT: I 47 GLU cc_start: 0.9101 (pm20) cc_final: 0.8379 (mt-10) REVERT: I 80 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8456 (tp) REVERT: I 82 MET cc_start: 0.9453 (mpp) cc_final: 0.8524 (mpp) REVERT: J 3 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8343 (tm-30) REVERT: J 46 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8489 (pm20) REVERT: J 73 ASN cc_start: 0.8217 (p0) cc_final: 0.7798 (p0) REVERT: J 82 ASP cc_start: 0.9435 (t0) cc_final: 0.9040 (m-30) REVERT: J 82 ASN cc_start: 0.9777 (OUTLIER) cc_final: 0.9079 (t0) REVERT: J 86 ASP cc_start: 0.9494 (m-30) cc_final: 0.9108 (m-30) REVERT: J 97 GLN cc_start: 0.9450 (mt0) cc_final: 0.9236 (mm110) REVERT: J 102 TYR cc_start: 0.9214 (m-80) cc_final: 0.8941 (m-10) outliers start: 52 outliers final: 33 residues processed: 263 average time/residue: 0.3570 time to fit residues: 141.5990 Evaluate side-chains 247 residues out of total 1864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 201 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 278 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 296 CYS 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 D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 150 MET 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 661 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 25 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 151 optimal weight: 0.0270 chunk 59 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 42 optimal weight: 0.0870 chunk 89 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 188 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 overall best weight: 1.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 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 = 0.2994 r_free = 0.2994 target = 0.047691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.035092 restraints weight = 86306.331| |-----------------------------------------------------------------------------| r_work (start): 0.2568 rms_B_bonded: 6.26 r_work: 0.2389 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.2389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3914 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= 0.153 Angle : 0.754 15.723 24717 Z= 0.373 Chirality : 0.045 0.248 2962 Planarity : 0.004 0.055 3042 Dihedral : 6.568 58.114 3849 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.52 % Favored : 91.33 % Rotamer: Outliers : 2.84 % Allowed : 32.89 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 2077 helix: 2.49 (0.29), residues: 311 sheet: -0.44 (0.21), residues: 654 loop : -1.35 (0.20), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 427 HIS 0.004 0.001 HIS E 216 PHE 0.030 0.001 PHE F 519 TYR 0.037 0.001 TYR J 102 ARG 0.009 0.000 ARG B 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 49) link_NAG-ASN : angle 2.08511 ( 147) link_BETA1-4 : bond 0.00292 ( 25) link_BETA1-4 : angle 1.19956 ( 75) link_ALPHA1-3 : bond 0.00737 ( 2) link_ALPHA1-3 : angle 2.49253 ( 6) hydrogen bonds : bond 0.03527 ( 534) hydrogen bonds : angle 4.16170 ( 1413) SS BOND : bond 0.00564 ( 39) SS BOND : angle 2.03648 ( 78) covalent geometry : bond 0.00370 (17991) covalent geometry : angle 0.72769 (24411) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8923.58 seconds wall clock time: 163 minutes 18.74 seconds (9798.74 seconds total)