Starting phenix.real_space_refine on Thu Mar 5 05:52:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsn_24675/03_2026/7rsn_24675.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.100 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 12333 2.51 5 N 3267 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19623 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "B" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "C" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "G" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 23, 'TRANS': 397} Chain breaks: 4 Chain: "I" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 995 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "H" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "L" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "E" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "F" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 978 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "K" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 795 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "C" 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: "G" 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 Time building chain proxies: 4.38, per 1000 atoms: 0.22 Number of scatterers: 19623 At special positions: 0 Unit cell: (148.03, 138.86, 120.52, 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 3900 8.00 N 3267 7.00 C 12333 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.07 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 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 A 501 " - pdb=" SG CYS B 605 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.07 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.02 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.07 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 4 " - " MAN N 5 " " MAN T 4 " - " MAN T 5 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 6 " " MAN c 4 " - " MAN c 5 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 6 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 601 " - " ASN A 463 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 332 " " NAG A 605 " - " ASN A 295 " " NAG A 606 " - " ASN A 301 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 230 " " NAG A 609 " - " ASN A 130 " " NAG A 610 " - " ASN A 355 " " NAG C 601 " - " ASN C 463 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 332 " " NAG C 605 " - " ASN C 295 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 230 " " NAG C 609 " - " ASN C 130 " " NAG C 610 " - " ASN C 355 " " NAG G 601 " - " ASN G 463 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 392 " " NAG G 604 " - " ASN G 332 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 230 " " NAG G 609 " - " ASN G 130 " " NAG G 610 " - " ASN G 355 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 197 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 197 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN C 156 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 241 " " NAG Y 1 " - " ASN G 276 " " NAG Z 1 " - " ASN G 197 " " NAG a 1 " - " ASN G 386 " " NAG b 1 " - " ASN G 156 " " NAG c 1 " - " ASN G 262 " " NAG d 1 " - " ASN G 241 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 811.7 milliseconds 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 45 sheets defined 20.1% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.621A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.997A pdb=" N ALA B 533 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN B 540 " --> pdb=" O ALA B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 594 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.804A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 664 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.621A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 535 removed outlier: 3.998A pdb=" N ALA D 533 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN D 540 " --> pdb=" O ALA D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 594 Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.805A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.620A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 335 through 353 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.568A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 530 through 535 removed outlier: 3.998A pdb=" N ALA I 533 " --> pdb=" O MET I 530 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N MET I 535 " --> pdb=" O ALA I 532 " (cutoff:3.500A) Processing helix chain 'I' and resid 536 through 542 removed outlier: 3.550A pdb=" N GLN I 540 " --> pdb=" O ALA I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 594 Processing helix chain 'I' and resid 618 through 622 Processing helix chain 'I' and resid 627 through 635 removed outlier: 3.804A pdb=" N ILE I 635 " --> pdb=" O TRP I 631 " (cutoff:3.500A) Processing helix chain 'I' and resid 645 through 664 Processing helix chain 'H' and resid 25 through 30 Processing helix chain 'H' and resid 60 through 65 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 25 through 30 Processing helix chain 'E' and resid 60 through 65 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 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 169 through 176 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.051A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.187A 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 274 removed outlier: 6.779A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL A 292 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N SER A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE A 468 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 176 Processing sheet with id=AB6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.050A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 3.508A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.779A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL C 292 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N THR C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE C 468 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AC2, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'G' and resid 169 through 176 Processing sheet with id=AC6, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.050A pdb=" N VAL G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N TYR G 435 " --> pdb=" O VAL G 200 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.509A pdb=" N GLY G 451 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.780A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N GLU G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N ASN G 448 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 10.052A pdb=" N VAL G 292 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N SER G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE G 468 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 304 through 312 removed outlier: 6.284A pdb=" N ARG G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU H 33 " --> pdb=" O LYS H 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS H 52 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AD8, first strand: chain 'E' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU E 33 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS E 52 " --> pdb=" O GLU E 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 35 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP E 50 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.147A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'F' and resid 10 through 12 removed outlier: 8.111A pdb=" N GLU F 33 " --> pdb=" O LYS F 52 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS F 52 " --> pdb=" O GLU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE F 35 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TRP F 50 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.340A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.148A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.148A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.40 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3721 1.32 - 1.45: 6278 1.45 - 1.59: 9770 1.59 - 1.72: 91 1.72 - 1.86: 165 Bond restraints: 20025 Sorted by residual: bond pdb=" CA SER A 132 " pdb=" C SER A 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 1.01e+02 bond pdb=" CA SER C 132 " pdb=" C SER C 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 1.00e+02 bond pdb=" CA SER G 132 " pdb=" C SER G 132 " ideal model delta sigma weight residual 1.520 1.568 -0.048 4.80e-03 4.34e+04 9.99e+01 bond pdb=" NE ARG G 504 " pdb=" CZ ARG G 504 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.53e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.408 -0.082 1.10e-02 8.26e+03 5.52e+01 ... (remaining 20020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.11: 27069 7.11 - 14.22: 90 14.22 - 21.33: 3 21.33 - 28.43: 0 28.43 - 35.54: 3 Bond angle restraints: 27165 Sorted by residual: angle pdb=" N PRO C 76 " pdb=" CA PRO C 76 " pdb=" C PRO C 76 " ideal model delta sigma weight residual 111.14 91.67 19.47 1.56e+00 4.11e-01 1.56e+02 angle pdb=" N PRO A 76 " pdb=" CA PRO A 76 " pdb=" C PRO A 76 " ideal model delta sigma weight residual 111.14 91.68 19.46 1.56e+00 4.11e-01 1.56e+02 angle pdb=" N PRO G 76 " pdb=" CA PRO G 76 " pdb=" C PRO G 76 " ideal model delta sigma weight residual 111.14 91.68 19.46 1.56e+00 4.11e-01 1.56e+02 angle pdb=" C2 NAG T 1 " pdb=" N2 NAG T 1 " pdb=" C7 NAG T 1 " ideal model delta sigma weight residual 124.56 160.10 -35.54 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 124.56 160.08 -35.52 3.00e+00 1.11e-01 1.40e+02 ... (remaining 27160 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 12768 21.12 - 42.24: 279 42.24 - 63.36: 78 63.36 - 84.48: 81 84.48 - 105.61: 48 Dihedral angle restraints: 13254 sinusoidal: 6621 harmonic: 6633 Sorted by residual: dihedral pdb=" CB CYS G 54 " pdb=" SG CYS G 54 " pdb=" SG CYS G 74 " pdb=" CB CYS G 74 " ideal model delta sinusoidal sigma weight residual -86.00 -172.70 86.70 1 1.00e+01 1.00e-02 9.05e+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 -172.69 86.69 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual -86.00 -172.67 86.67 1 1.00e+01 1.00e-02 9.04e+01 ... (remaining 13251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2401 0.124 - 0.247: 602 0.247 - 0.371: 240 0.371 - 0.495: 69 0.495 - 0.618: 6 Chirality restraints: 3318 Sorted by residual: chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.41e+02 chirality pdb=" C1 NAG Y 2 " pdb=" O4 NAG Y 1 " pdb=" C2 NAG Y 2 " pdb=" O5 NAG Y 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.38e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 ... (remaining 3315 not shown) Planarity restraints: 3357 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 230 " -0.095 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN C 230 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN C 230 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 230 " 0.156 2.00e-02 2.50e+03 pdb=" C1 NAG C 608 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 230 " 0.095 2.00e-02 2.50e+03 1.00e-01 1.25e+02 pdb=" CG ASN A 230 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 230 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 230 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 230 " 0.095 2.00e-02 2.50e+03 9.99e-02 1.25e+02 pdb=" CG ASN G 230 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN G 230 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN G 230 " -0.156 2.00e-02 2.50e+03 pdb=" C1 NAG G 608 " 0.122 2.00e-02 2.50e+03 ... (remaining 3354 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5001 2.82 - 3.34: 17496 3.34 - 3.86: 32091 3.86 - 4.38: 38694 4.38 - 4.90: 61517 Nonbonded interactions: 154799 Sorted by model distance: nonbonded pdb=" N PRO A 76 " pdb=" O PRO A 76 " model vdw 2.296 2.496 nonbonded pdb=" N PRO C 76 " pdb=" O PRO C 76 " model vdw 2.296 2.496 nonbonded pdb=" N PRO G 76 " pdb=" O PRO G 76 " model vdw 2.297 2.496 nonbonded pdb=" N ASN C 234 " pdb=" OD1 ASN C 234 " model vdw 2.440 3.120 nonbonded pdb=" N ASN G 234 " pdb=" OD1 ASN G 234 " model vdw 2.440 3.120 ... (remaining 154794 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'Y' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.820 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.023 0.125 20160 Z= 1.238 Angle : 1.877 35.542 27534 Z= 1.177 Chirality : 0.138 0.618 3318 Planarity : 0.009 0.060 3309 Dihedral : 13.448 105.606 8862 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 0.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 3.99 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.17), residues: 2256 helix: 0.26 (0.23), residues: 354 sheet: 1.00 (0.19), residues: 735 loop : -0.01 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 61 TYR 0.032 0.007 TYR A 318 PHE 0.032 0.006 PHE A 353 TRP 0.056 0.011 TRP I 610 HIS 0.011 0.003 HIS K 32 Details of bonding type rmsd covalent geometry : bond 0.02274 (20025) covalent geometry : angle 1.84264 (27165) SS BOND : bond 0.01335 ( 36) SS BOND : angle 2.42274 ( 72) hydrogen bonds : bond 0.15149 ( 714) hydrogen bonds : angle 7.39503 ( 1890) link_ALPHA1-2 : bond 0.08233 ( 3) link_ALPHA1-2 : angle 5.70618 ( 9) link_ALPHA1-3 : bond 0.08932 ( 12) link_ALPHA1-3 : angle 4.69159 ( 36) link_ALPHA1-6 : bond 0.05787 ( 9) link_ALPHA1-6 : angle 2.64517 ( 27) link_BETA1-4 : bond 0.07664 ( 27) link_BETA1-4 : angle 5.29143 ( 81) link_NAG-ASN : bond 0.08162 ( 48) link_NAG-ASN : angle 2.35686 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8863 (m-80) cc_final: 0.8331 (m-10) REVERT: A 217 TYR cc_start: 0.8840 (m-80) cc_final: 0.7371 (m-80) REVERT: B 650 GLN cc_start: 0.7695 (tp40) cc_final: 0.7265 (tm-30) REVERT: C 180 ASP cc_start: 0.7875 (m-30) cc_final: 0.7628 (m-30) REVERT: C 316 TRP cc_start: 0.7469 (p90) cc_final: 0.7128 (p90) REVERT: C 502 LYS cc_start: 0.8439 (tttt) cc_final: 0.8217 (mttm) REVERT: G 217 TYR cc_start: 0.8853 (m-80) cc_final: 0.8368 (m-80) REVERT: L 42 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7830 (mm-40) REVERT: E 68 SER cc_start: 0.8916 (t) cc_final: 0.8626 (p) REVERT: J 42 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7637 (mm110) REVERT: F 68 SER cc_start: 0.8846 (t) cc_final: 0.8625 (p) REVERT: K 14 SER cc_start: 0.7452 (m) cc_final: 0.7131 (p) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.1654 time to fit residues: 150.9767 Evaluate side-chains 298 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 203 GLN A 344 GLN B 590 GLN C 105 HIS C 114 GLN C 344 GLN D 590 GLN G 105 HIS G 203 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS E 65 GLN E 79 HIS F 65 GLN F 79 HIS K 66 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.141541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112973 restraints weight = 31535.745| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.30 r_work: 0.3251 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20160 Z= 0.190 Angle : 0.851 18.498 27534 Z= 0.410 Chirality : 0.052 0.408 3318 Planarity : 0.005 0.056 3309 Dihedral : 10.703 76.385 4488 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.12 % Favored : 95.74 % Rotamer: Outliers : 2.27 % Allowed : 8.48 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 2256 helix: 1.60 (0.28), residues: 381 sheet: 0.41 (0.18), residues: 786 loop : -0.31 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 444 TYR 0.019 0.002 TYR J 86 PHE 0.019 0.002 PHE A 233 TRP 0.017 0.002 TRP C 479 HIS 0.006 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00423 (20025) covalent geometry : angle 0.79510 (27165) SS BOND : bond 0.00384 ( 36) SS BOND : angle 0.95347 ( 72) hydrogen bonds : bond 0.05046 ( 714) hydrogen bonds : angle 6.07416 ( 1890) link_ALPHA1-2 : bond 0.01880 ( 3) link_ALPHA1-2 : angle 4.37232 ( 9) link_ALPHA1-3 : bond 0.01027 ( 12) link_ALPHA1-3 : angle 1.99250 ( 36) link_ALPHA1-6 : bond 0.00901 ( 9) link_ALPHA1-6 : angle 1.45704 ( 27) link_BETA1-4 : bond 0.00984 ( 27) link_BETA1-4 : angle 3.77043 ( 81) link_NAG-ASN : bond 0.00893 ( 48) link_NAG-ASN : angle 2.86607 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 395 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8770 (mtp85) cc_final: 0.8235 (ttm110) REVERT: A 177 TYR cc_start: 0.8829 (m-80) cc_final: 0.8564 (m-80) REVERT: A 191 TYR cc_start: 0.9085 (m-80) cc_final: 0.8845 (m-10) REVERT: A 217 TYR cc_start: 0.8854 (m-80) cc_final: 0.7199 (m-80) REVERT: A 293 GLU cc_start: 0.8562 (tt0) cc_final: 0.7805 (pp20) REVERT: A 446 SER cc_start: 0.9187 (t) cc_final: 0.8945 (p) REVERT: B 535 MET cc_start: 0.8389 (mpp) cc_final: 0.7876 (mmm) REVERT: B 620 ASP cc_start: 0.6943 (p0) cc_final: 0.6540 (p0) REVERT: B 635 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6458 (mt) REVERT: C 113 ASP cc_start: 0.8407 (t70) cc_final: 0.8173 (m-30) REVERT: C 173 TYR cc_start: 0.8748 (m-80) cc_final: 0.8524 (m-80) REVERT: C 210 PHE cc_start: 0.8556 (m-10) cc_final: 0.8294 (m-10) REVERT: C 269 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7122 (mm-30) REVERT: C 293 GLU cc_start: 0.8553 (tt0) cc_final: 0.8072 (pp20) REVERT: C 316 TRP cc_start: 0.7273 (p90) cc_final: 0.6865 (p90) REVERT: C 502 LYS cc_start: 0.8231 (tttt) cc_final: 0.7718 (mmtm) REVERT: G 166 ARG cc_start: 0.9011 (mtp85) cc_final: 0.8678 (mtm180) REVERT: G 293 GLU cc_start: 0.8397 (tt0) cc_final: 0.7733 (pp20) REVERT: G 315 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6799 (mtm-85) REVERT: G 427 TRP cc_start: 0.7558 (m-90) cc_final: 0.7352 (m-90) REVERT: G 460 LYS cc_start: 0.8908 (tptt) cc_final: 0.8700 (ttpp) REVERT: I 603 ILE cc_start: 0.8182 (mp) cc_final: 0.7933 (mp) REVERT: H 65 GLN cc_start: 0.9017 (tt0) cc_final: 0.8692 (tp40) REVERT: L 42 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7839 (mm-40) REVERT: J 42 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7729 (mm110) REVERT: F 65 GLN cc_start: 0.8775 (tt0) cc_final: 0.8534 (tp40) REVERT: F 80 MET cc_start: 0.8803 (ttt) cc_final: 0.8492 (ttt) REVERT: F 96 LYS cc_start: 0.8344 (mtmt) cc_final: 0.7775 (mtmm) REVERT: K 17 GLU cc_start: 0.8176 (tp30) cc_final: 0.7867 (tp30) REVERT: K 37 GLN cc_start: 0.8203 (tt0) cc_final: 0.7821 (tt0) REVERT: K 96 GLU cc_start: 0.9171 (pt0) cc_final: 0.8918 (pt0) outliers start: 46 outliers final: 25 residues processed: 422 average time/residue: 0.1402 time to fit residues: 89.3813 Evaluate side-chains 342 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 316 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109687 restraints weight = 30134.888| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.78 r_work: 0.3211 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20160 Z= 0.205 Angle : 0.765 17.561 27534 Z= 0.368 Chirality : 0.048 0.255 3318 Planarity : 0.005 0.056 3309 Dihedral : 9.453 70.794 4488 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 3.16 % Allowed : 8.93 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.18), residues: 2256 helix: 1.69 (0.28), residues: 378 sheet: 0.20 (0.17), residues: 834 loop : -0.57 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 107 TYR 0.017 0.002 TYR J 86 PHE 0.020 0.002 PHE C 376 TRP 0.018 0.002 TRP F 50 HIS 0.004 0.002 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00469 (20025) covalent geometry : angle 0.72425 (27165) SS BOND : bond 0.00643 ( 36) SS BOND : angle 0.74382 ( 72) hydrogen bonds : bond 0.04252 ( 714) hydrogen bonds : angle 5.59717 ( 1890) link_ALPHA1-2 : bond 0.01521 ( 3) link_ALPHA1-2 : angle 5.08497 ( 9) link_ALPHA1-3 : bond 0.01087 ( 12) link_ALPHA1-3 : angle 1.50152 ( 36) link_ALPHA1-6 : bond 0.00658 ( 9) link_ALPHA1-6 : angle 1.44090 ( 27) link_BETA1-4 : bond 0.00959 ( 27) link_BETA1-4 : angle 2.92095 ( 81) link_NAG-ASN : bond 0.00661 ( 48) link_NAG-ASN : angle 2.27306 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 375 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.9029 (m-80) cc_final: 0.8816 (m-80) REVERT: A 217 TYR cc_start: 0.9030 (m-80) cc_final: 0.7352 (m-80) REVERT: B 615 SER cc_start: 0.6816 (t) cc_final: 0.6554 (p) REVERT: B 635 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6741 (mt) REVERT: B 651 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7942 (t0) REVERT: C 173 TYR cc_start: 0.8661 (m-80) cc_final: 0.8431 (m-80) REVERT: C 191 TYR cc_start: 0.9028 (m-80) cc_final: 0.8470 (m-80) REVERT: C 316 TRP cc_start: 0.7416 (p90) cc_final: 0.7066 (p90) REVERT: C 502 LYS cc_start: 0.8337 (tttt) cc_final: 0.8110 (tttp) REVERT: D 530 MET cc_start: 0.6721 (mtp) cc_final: 0.6432 (mtp) REVERT: G 166 ARG cc_start: 0.8881 (mtp85) cc_final: 0.8098 (mtm180) REVERT: G 446 SER cc_start: 0.9215 (t) cc_final: 0.8935 (p) REVERT: I 651 ASN cc_start: 0.7981 (t0) cc_final: 0.7706 (t0) REVERT: H 38 ARG cc_start: 0.8723 (ttp-170) cc_final: 0.8516 (ttp80) REVERT: H 62 ASP cc_start: 0.8110 (m-30) cc_final: 0.7811 (t0) REVERT: H 100 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8247 (mt0) REVERT: L 42 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7720 (mm-40) REVERT: E 62 ASP cc_start: 0.7928 (m-30) cc_final: 0.7641 (t0) REVERT: E 100 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8312 (mt0) REVERT: J 42 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7663 (mm110) REVERT: F 26 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7254 (tm-30) REVERT: F 62 ASP cc_start: 0.8015 (m-30) cc_final: 0.7662 (t0) REVERT: F 80 MET cc_start: 0.8746 (ttt) cc_final: 0.8456 (ttt) REVERT: F 100 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8316 (mt0) REVERT: K 17 GLU cc_start: 0.8217 (tp30) cc_final: 0.7859 (tp30) REVERT: K 37 GLN cc_start: 0.8446 (tt0) cc_final: 0.8024 (tt0) outliers start: 64 outliers final: 44 residues processed: 403 average time/residue: 0.1344 time to fit residues: 82.1603 Evaluate side-chains 366 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 320 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 635 ILE Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 78 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 92 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 ASN C 302 ASN C 377 ASN G 377 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106990 restraints weight = 30377.428| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.88 r_work: 0.3144 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20160 Z= 0.221 Angle : 0.740 13.577 27534 Z= 0.356 Chirality : 0.049 0.259 3318 Planarity : 0.005 0.061 3309 Dihedral : 8.772 65.426 4488 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.52 % Favored : 95.17 % Rotamer: Outliers : 2.86 % Allowed : 10.85 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.18), residues: 2256 helix: 1.65 (0.28), residues: 381 sheet: 0.04 (0.18), residues: 822 loop : -0.82 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 504 TYR 0.015 0.002 TYR F 98 PHE 0.022 0.002 PHE C 376 TRP 0.022 0.002 TRP C 35 HIS 0.005 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00516 (20025) covalent geometry : angle 0.70281 (27165) SS BOND : bond 0.00478 ( 36) SS BOND : angle 0.82126 ( 72) hydrogen bonds : bond 0.03974 ( 714) hydrogen bonds : angle 5.43439 ( 1890) link_ALPHA1-2 : bond 0.01552 ( 3) link_ALPHA1-2 : angle 5.07103 ( 9) link_ALPHA1-3 : bond 0.01056 ( 12) link_ALPHA1-3 : angle 1.78464 ( 36) link_ALPHA1-6 : bond 0.00566 ( 9) link_ALPHA1-6 : angle 1.56744 ( 27) link_BETA1-4 : bond 0.00799 ( 27) link_BETA1-4 : angle 2.69613 ( 81) link_NAG-ASN : bond 0.00411 ( 48) link_NAG-ASN : angle 2.07791 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 351 time to evaluate : 0.679 Fit side-chains REVERT: A 191 TYR cc_start: 0.9012 (m-80) cc_final: 0.8787 (m-80) REVERT: A 217 TYR cc_start: 0.8906 (m-80) cc_final: 0.7446 (m-80) REVERT: B 635 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 651 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7947 (t0) REVERT: C 173 TYR cc_start: 0.8618 (m-80) cc_final: 0.8404 (m-80) REVERT: C 191 TYR cc_start: 0.9073 (m-80) cc_final: 0.8818 (m-80) REVERT: G 166 ARG cc_start: 0.8755 (mtp85) cc_final: 0.8327 (mtm180) REVERT: G 427 TRP cc_start: 0.7789 (m-90) cc_final: 0.7347 (m-90) REVERT: G 446 SER cc_start: 0.9351 (t) cc_final: 0.8974 (p) REVERT: I 615 SER cc_start: 0.7016 (t) cc_final: 0.6708 (p) REVERT: H 62 ASP cc_start: 0.8287 (m-30) cc_final: 0.7944 (t0) REVERT: H 100 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8307 (mt0) REVERT: L 14 SER cc_start: 0.7634 (t) cc_final: 0.7136 (p) REVERT: L 42 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7722 (mm-40) REVERT: E 62 ASP cc_start: 0.8128 (m-30) cc_final: 0.7883 (t0) REVERT: E 100 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8390 (mt0) REVERT: J 42 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7664 (mm110) REVERT: J 100 GLN cc_start: 0.8867 (mp10) cc_final: 0.8583 (mp10) REVERT: F 26 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7222 (tm-30) REVERT: F 62 ASP cc_start: 0.8148 (m-30) cc_final: 0.7895 (t0) REVERT: F 100 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8309 (mm-40) REVERT: K 17 GLU cc_start: 0.8315 (tp30) cc_final: 0.8011 (tp30) REVERT: K 37 GLN cc_start: 0.8523 (tt0) cc_final: 0.7980 (tt0) outliers start: 58 outliers final: 36 residues processed: 383 average time/residue: 0.1390 time to fit residues: 80.6430 Evaluate side-chains 363 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 325 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 chunk 111 optimal weight: 0.0970 chunk 12 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.1580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN C 377 ASN D 590 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108673 restraints weight = 29970.455| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.69 r_work: 0.3191 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20160 Z= 0.149 Angle : 0.680 12.529 27534 Z= 0.324 Chirality : 0.047 0.275 3318 Planarity : 0.005 0.062 3309 Dihedral : 8.194 61.549 4488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.34 % Favored : 95.30 % Rotamer: Outliers : 2.42 % Allowed : 11.79 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.18), residues: 2256 helix: 1.59 (0.27), residues: 399 sheet: 0.10 (0.18), residues: 825 loop : -0.97 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 31 TYR 0.012 0.001 TYR J 86 PHE 0.017 0.001 PHE C 376 TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00336 (20025) covalent geometry : angle 0.64243 (27165) SS BOND : bond 0.00550 ( 36) SS BOND : angle 0.65623 ( 72) hydrogen bonds : bond 0.03510 ( 714) hydrogen bonds : angle 5.24758 ( 1890) link_ALPHA1-2 : bond 0.01598 ( 3) link_ALPHA1-2 : angle 5.21370 ( 9) link_ALPHA1-3 : bond 0.01153 ( 12) link_ALPHA1-3 : angle 1.66464 ( 36) link_ALPHA1-6 : bond 0.00603 ( 9) link_ALPHA1-6 : angle 1.58547 ( 27) link_BETA1-4 : bond 0.00819 ( 27) link_BETA1-4 : angle 2.45177 ( 81) link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.05369 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 351 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7145 (mm-30) REVERT: A 191 TYR cc_start: 0.8928 (m-80) cc_final: 0.8663 (m-80) REVERT: A 217 TYR cc_start: 0.8874 (m-80) cc_final: 0.7567 (m-80) REVERT: B 635 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7394 (mt) REVERT: C 173 TYR cc_start: 0.8588 (m-80) cc_final: 0.8374 (m-80) REVERT: C 191 TYR cc_start: 0.9050 (m-80) cc_final: 0.8772 (m-80) REVERT: C 347 ASN cc_start: 0.8889 (t0) cc_final: 0.8544 (t0) REVERT: G 166 ARG cc_start: 0.8598 (mtp85) cc_final: 0.8121 (mtp85) REVERT: G 446 SER cc_start: 0.9348 (t) cc_final: 0.8937 (p) REVERT: I 603 ILE cc_start: 0.8409 (mp) cc_final: 0.8090 (mp) REVERT: I 620 ASP cc_start: 0.7709 (p0) cc_final: 0.7175 (p0) REVERT: I 651 ASN cc_start: 0.7530 (t0) cc_final: 0.7312 (t0) REVERT: H 6 GLN cc_start: 0.8520 (mt0) cc_final: 0.8209 (tt0) REVERT: H 62 ASP cc_start: 0.8308 (m-30) cc_final: 0.8000 (t0) REVERT: H 100 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8283 (mt0) REVERT: L 42 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7667 (mm-40) REVERT: E 100 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8348 (mt0) REVERT: J 42 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7980 (mt0) REVERT: F 26 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7220 (tm-30) REVERT: F 100 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8299 (mm-40) REVERT: K 17 GLU cc_start: 0.8260 (tp30) cc_final: 0.7981 (tp30) REVERT: K 37 GLN cc_start: 0.8521 (tt0) cc_final: 0.7967 (tt0) outliers start: 49 outliers final: 37 residues processed: 377 average time/residue: 0.1408 time to fit residues: 80.9958 Evaluate side-chains 360 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 322 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 78 MET Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 35 optimal weight: 0.0770 chunk 164 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103649 restraints weight = 30245.286| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.66 r_work: 0.3124 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20160 Z= 0.286 Angle : 0.780 14.344 27534 Z= 0.378 Chirality : 0.050 0.254 3318 Planarity : 0.005 0.062 3309 Dihedral : 8.352 60.614 4488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.03 % Favored : 93.71 % Rotamer: Outliers : 3.25 % Allowed : 12.18 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 1.96 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.18), residues: 2256 helix: 1.68 (0.27), residues: 381 sheet: -0.08 (0.18), residues: 813 loop : -1.22 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 107 TYR 0.015 0.002 TYR C 217 PHE 0.024 0.002 PHE A 376 TRP 0.019 0.003 TRP F 23 HIS 0.008 0.003 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00677 (20025) covalent geometry : angle 0.74588 (27165) SS BOND : bond 0.00544 ( 36) SS BOND : angle 0.85012 ( 72) hydrogen bonds : bond 0.04145 ( 714) hydrogen bonds : angle 5.39084 ( 1890) link_ALPHA1-2 : bond 0.01461 ( 3) link_ALPHA1-2 : angle 5.18575 ( 9) link_ALPHA1-3 : bond 0.00971 ( 12) link_ALPHA1-3 : angle 1.79787 ( 36) link_ALPHA1-6 : bond 0.00496 ( 9) link_ALPHA1-6 : angle 1.57198 ( 27) link_BETA1-4 : bond 0.00769 ( 27) link_BETA1-4 : angle 2.54461 ( 81) link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.07062 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 339 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8940 (m-80) cc_final: 0.8610 (m-80) REVERT: C 173 TYR cc_start: 0.8584 (m-80) cc_final: 0.8379 (m-80) REVERT: C 191 TYR cc_start: 0.9028 (m-80) cc_final: 0.8708 (m-10) REVERT: C 347 ASN cc_start: 0.8961 (t0) cc_final: 0.8646 (t0) REVERT: D 530 MET cc_start: 0.6933 (mtp) cc_final: 0.6565 (ttt) REVERT: D 577 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: D 655 LYS cc_start: 0.8762 (tptp) cc_final: 0.7820 (pttt) REVERT: G 166 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8323 (mtp85) REVERT: G 446 SER cc_start: 0.9450 (t) cc_final: 0.9087 (p) REVERT: I 603 ILE cc_start: 0.8506 (mp) cc_final: 0.8237 (mm) REVERT: H 26 GLU cc_start: 0.7830 (tt0) cc_final: 0.7501 (tm-30) REVERT: L 14 SER cc_start: 0.7765 (t) cc_final: 0.7263 (p) REVERT: F 26 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7315 (tm-30) REVERT: F 100 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8445 (mm-40) REVERT: K 37 GLN cc_start: 0.8617 (tt0) cc_final: 0.8009 (tt0) outliers start: 66 outliers final: 50 residues processed: 374 average time/residue: 0.1485 time to fit residues: 82.8370 Evaluate side-chains 379 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 328 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 388 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain D residue 621 GLU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 377 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108053 restraints weight = 30002.531| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.63 r_work: 0.3188 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20160 Z= 0.135 Angle : 0.668 12.102 27534 Z= 0.320 Chirality : 0.047 0.240 3318 Planarity : 0.005 0.062 3309 Dihedral : 7.770 57.921 4488 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.74 % Favored : 94.99 % Rotamer: Outliers : 2.02 % Allowed : 13.46 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.18), residues: 2256 helix: 1.64 (0.27), residues: 402 sheet: -0.03 (0.18), residues: 798 loop : -1.20 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 94 TYR 0.018 0.001 TYR B 638 PHE 0.017 0.001 PHE C 376 TRP 0.018 0.002 TRP F 50 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00304 (20025) covalent geometry : angle 0.63239 (27165) SS BOND : bond 0.00389 ( 36) SS BOND : angle 0.75489 ( 72) hydrogen bonds : bond 0.03397 ( 714) hydrogen bonds : angle 5.18121 ( 1890) link_ALPHA1-2 : bond 0.01610 ( 3) link_ALPHA1-2 : angle 5.34399 ( 9) link_ALPHA1-3 : bond 0.01164 ( 12) link_ALPHA1-3 : angle 1.61603 ( 36) link_ALPHA1-6 : bond 0.00568 ( 9) link_ALPHA1-6 : angle 1.60833 ( 27) link_BETA1-4 : bond 0.00800 ( 27) link_BETA1-4 : angle 2.31566 ( 81) link_NAG-ASN : bond 0.00374 ( 48) link_NAG-ASN : angle 1.88591 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 353 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8916 (m-80) cc_final: 0.8596 (m-80) REVERT: C 173 TYR cc_start: 0.8569 (m-80) cc_final: 0.8347 (m-80) REVERT: C 191 TYR cc_start: 0.8995 (m-80) cc_final: 0.8734 (m-80) REVERT: C 347 ASN cc_start: 0.8930 (t0) cc_final: 0.8555 (t0) REVERT: C 502 LYS cc_start: 0.8027 (tttm) cc_final: 0.6995 (mtpt) REVERT: D 530 MET cc_start: 0.6795 (mtp) cc_final: 0.6474 (ttt) REVERT: D 655 LYS cc_start: 0.8738 (tptp) cc_final: 0.7802 (pttt) REVERT: G 166 ARG cc_start: 0.8602 (mtp85) cc_final: 0.8115 (mtp85) REVERT: G 446 SER cc_start: 0.9425 (t) cc_final: 0.9057 (p) REVERT: H 26 GLU cc_start: 0.7772 (tt0) cc_final: 0.7462 (tm-30) REVERT: H 33 GLU cc_start: 0.8546 (tt0) cc_final: 0.8177 (tt0) REVERT: H 43 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8635 (mp10) REVERT: H 96 LYS cc_start: 0.8407 (mtmt) cc_final: 0.8178 (mtmt) REVERT: H 100 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8221 (mt0) REVERT: L 42 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8102 (mm-40) REVERT: E 43 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8847 (mp10) REVERT: E 74 ASP cc_start: 0.8631 (m-30) cc_final: 0.8376 (m-30) REVERT: E 100 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8415 (mt0) REVERT: J 42 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7983 (mt0) REVERT: J 54 ARG cc_start: 0.8537 (ptp90) cc_final: 0.8241 (ptp90) REVERT: F 26 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7284 (tm-30) REVERT: F 43 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8801 (mm-40) REVERT: F 100 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8359 (mm-40) REVERT: K 37 GLN cc_start: 0.8525 (tt0) cc_final: 0.8011 (tt0) REVERT: K 82 ASP cc_start: 0.8254 (m-30) cc_final: 0.7962 (m-30) outliers start: 41 outliers final: 31 residues processed: 374 average time/residue: 0.1524 time to fit residues: 85.3688 Evaluate side-chains 364 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 333 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 79 optimal weight: 0.0770 chunk 45 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 122 optimal weight: 1.9990 overall best weight: 0.7152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN C 363 GLN G 343 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109364 restraints weight = 29965.748| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.65 r_work: 0.3209 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20160 Z= 0.126 Angle : 0.647 8.687 27534 Z= 0.309 Chirality : 0.046 0.234 3318 Planarity : 0.004 0.063 3309 Dihedral : 7.410 57.744 4488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.23 % Favored : 94.50 % Rotamer: Outliers : 2.02 % Allowed : 13.76 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 2256 helix: 1.91 (0.28), residues: 381 sheet: 0.03 (0.18), residues: 798 loop : -1.13 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 82A TYR 0.018 0.001 TYR B 638 PHE 0.015 0.001 PHE C 376 TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS K 32 Details of bonding type rmsd covalent geometry : bond 0.00282 (20025) covalent geometry : angle 0.61205 (27165) SS BOND : bond 0.00300 ( 36) SS BOND : angle 0.71137 ( 72) hydrogen bonds : bond 0.03155 ( 714) hydrogen bonds : angle 5.04978 ( 1890) link_ALPHA1-2 : bond 0.01494 ( 3) link_ALPHA1-2 : angle 5.32473 ( 9) link_ALPHA1-3 : bond 0.01066 ( 12) link_ALPHA1-3 : angle 1.59011 ( 36) link_ALPHA1-6 : bond 0.00583 ( 9) link_ALPHA1-6 : angle 1.65084 ( 27) link_BETA1-4 : bond 0.00776 ( 27) link_BETA1-4 : angle 2.27301 ( 81) link_NAG-ASN : bond 0.00359 ( 48) link_NAG-ASN : angle 1.79265 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 363 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8911 (m-80) cc_final: 0.8503 (m-10) REVERT: C 173 TYR cc_start: 0.8524 (m-80) cc_final: 0.8293 (m-80) REVERT: C 191 TYR cc_start: 0.9027 (m-80) cc_final: 0.8750 (m-80) REVERT: C 347 ASN cc_start: 0.8939 (t0) cc_final: 0.8540 (t0) REVERT: C 502 LYS cc_start: 0.8027 (tttm) cc_final: 0.6982 (mtpt) REVERT: D 530 MET cc_start: 0.6768 (mtp) cc_final: 0.6473 (ttt) REVERT: D 588 LYS cc_start: 0.8652 (tptt) cc_final: 0.8439 (tppt) REVERT: D 655 LYS cc_start: 0.8707 (tptp) cc_final: 0.7892 (pttt) REVERT: G 113 ASP cc_start: 0.8736 (t0) cc_final: 0.8031 (m-30) REVERT: G 166 ARG cc_start: 0.8765 (mtp85) cc_final: 0.8403 (mtp85) REVERT: G 446 SER cc_start: 0.9409 (t) cc_final: 0.9048 (p) REVERT: H 26 GLU cc_start: 0.7770 (tt0) cc_final: 0.7466 (tm-30) REVERT: H 33 GLU cc_start: 0.8440 (tt0) cc_final: 0.8080 (tt0) REVERT: H 43 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8583 (mp10) REVERT: H 100 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8234 (mt0) REVERT: L 54 ARG cc_start: 0.8596 (ptp90) cc_final: 0.7956 (ptp90) REVERT: E 43 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8796 (mp10) REVERT: E 74 ASP cc_start: 0.8582 (m-30) cc_final: 0.8317 (m-30) REVERT: E 100 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8398 (mt0) REVERT: J 33 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: J 42 GLN cc_start: 0.8278 (mm-40) cc_final: 0.7942 (mt0) REVERT: J 54 ARG cc_start: 0.8531 (ptp90) cc_final: 0.8234 (ptp90) REVERT: F 26 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7257 (tm-30) REVERT: F 43 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8737 (mm-40) REVERT: F 100 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8324 (mm-40) REVERT: K 37 GLN cc_start: 0.8577 (tt0) cc_final: 0.8020 (tt0) REVERT: K 82 ASP cc_start: 0.8207 (m-30) cc_final: 0.7884 (m-30) outliers start: 41 outliers final: 33 residues processed: 383 average time/residue: 0.1489 time to fit residues: 85.9838 Evaluate side-chains 366 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 332 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 104 LEU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN C 80 ASN C 82 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101188 restraints weight = 30609.315| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.82 r_work: 0.3083 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 20160 Z= 0.377 Angle : 0.859 10.740 27534 Z= 0.420 Chirality : 0.053 0.261 3318 Planarity : 0.005 0.052 3309 Dihedral : 8.292 57.086 4488 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.40 % Favored : 92.33 % Rotamer: Outliers : 2.66 % Allowed : 13.41 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2256 helix: 1.29 (0.26), residues: 402 sheet: -0.23 (0.18), residues: 828 loop : -1.46 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 94 TYR 0.033 0.003 TYR B 638 PHE 0.026 0.003 PHE G 376 TRP 0.031 0.003 TRP G 427 HIS 0.009 0.003 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00897 (20025) covalent geometry : angle 0.82531 (27165) SS BOND : bond 0.00629 ( 36) SS BOND : angle 0.97286 ( 72) hydrogen bonds : bond 0.04538 ( 714) hydrogen bonds : angle 5.47988 ( 1890) link_ALPHA1-2 : bond 0.01396 ( 3) link_ALPHA1-2 : angle 5.15533 ( 9) link_ALPHA1-3 : bond 0.00853 ( 12) link_ALPHA1-3 : angle 1.89003 ( 36) link_ALPHA1-6 : bond 0.00418 ( 9) link_ALPHA1-6 : angle 1.60679 ( 27) link_BETA1-4 : bond 0.00771 ( 27) link_BETA1-4 : angle 2.61062 ( 81) link_NAG-ASN : bond 0.00479 ( 48) link_NAG-ASN : angle 2.26221 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8949 (m-80) cc_final: 0.8644 (m-80) REVERT: B 535 MET cc_start: 0.8132 (mpp) cc_final: 0.7766 (mmm) REVERT: B 634 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7717 (tt0) REVERT: C 173 TYR cc_start: 0.8595 (m-80) cc_final: 0.8365 (m-80) REVERT: C 191 TYR cc_start: 0.8996 (m-80) cc_final: 0.8683 (m-10) REVERT: C 347 ASN cc_start: 0.8956 (t0) cc_final: 0.8606 (t0) REVERT: C 457 ASP cc_start: 0.8028 (t0) cc_final: 0.7824 (t0) REVERT: D 530 MET cc_start: 0.6970 (mtp) cc_final: 0.6732 (ttt) REVERT: D 577 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8250 (tp40) REVERT: D 655 LYS cc_start: 0.8764 (tptp) cc_final: 0.7891 (pttt) REVERT: G 166 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8311 (mtp85) REVERT: G 446 SER cc_start: 0.9424 (t) cc_final: 0.9153 (p) REVERT: I 603 ILE cc_start: 0.8743 (mp) cc_final: 0.8357 (mp) REVERT: I 651 ASN cc_start: 0.7875 (t0) cc_final: 0.7652 (t0) REVERT: H 26 GLU cc_start: 0.7918 (tt0) cc_final: 0.7609 (tm-30) REVERT: H 33 GLU cc_start: 0.8515 (tt0) cc_final: 0.8162 (tt0) REVERT: H 65 GLN cc_start: 0.8888 (tp40) cc_final: 0.8475 (tp-100) REVERT: L 14 SER cc_start: 0.7757 (t) cc_final: 0.7360 (p) REVERT: L 54 ARG cc_start: 0.8672 (ptp90) cc_final: 0.8083 (ptp90) REVERT: E 43 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8815 (mp10) REVERT: E 100 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8601 (mt0) REVERT: J 14 SER cc_start: 0.7592 (OUTLIER) cc_final: 0.7126 (p) REVERT: J 42 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8053 (mt0) REVERT: F 26 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7420 (tm-30) REVERT: F 84 GLN cc_start: 0.8232 (tt0) cc_final: 0.7994 (tt0) REVERT: F 100 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8434 (mm-40) REVERT: K 37 GLN cc_start: 0.8659 (tt0) cc_final: 0.8126 (tt0) REVERT: K 82 ASP cc_start: 0.7999 (m-30) cc_final: 0.7719 (m-30) outliers start: 54 outliers final: 42 residues processed: 368 average time/residue: 0.1581 time to fit residues: 85.9013 Evaluate side-chains 373 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain C residue 66 ARG Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain D residue 577 GLN Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 529 THR Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 151 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 154 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.107395 restraints weight = 29976.389| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.63 r_work: 0.3179 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20160 Z= 0.135 Angle : 0.687 9.624 27534 Z= 0.331 Chirality : 0.047 0.242 3318 Planarity : 0.005 0.060 3309 Dihedral : 7.654 58.234 4488 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.79 % Favored : 94.95 % Rotamer: Outliers : 1.53 % Allowed : 15.09 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.18), residues: 2256 helix: 1.30 (0.26), residues: 420 sheet: -0.13 (0.18), residues: 804 loop : -1.39 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 579 TYR 0.024 0.001 TYR B 638 PHE 0.017 0.001 PHE C 376 TRP 0.023 0.002 TRP G 427 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00299 (20025) covalent geometry : angle 0.65251 (27165) SS BOND : bond 0.00451 ( 36) SS BOND : angle 0.74622 ( 72) hydrogen bonds : bond 0.03387 ( 714) hydrogen bonds : angle 5.17005 ( 1890) link_ALPHA1-2 : bond 0.01727 ( 3) link_ALPHA1-2 : angle 5.40707 ( 9) link_ALPHA1-3 : bond 0.01209 ( 12) link_ALPHA1-3 : angle 1.57188 ( 36) link_ALPHA1-6 : bond 0.00528 ( 9) link_ALPHA1-6 : angle 1.62856 ( 27) link_BETA1-4 : bond 0.00821 ( 27) link_BETA1-4 : angle 2.27414 ( 81) link_NAG-ASN : bond 0.00419 ( 48) link_NAG-ASN : angle 1.93464 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4512 Ramachandran restraints generated. 2256 Oldfield, 0 Emsley, 2256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 88 ASN cc_start: 0.8740 (t0) cc_final: 0.8452 (t0) REVERT: A 191 TYR cc_start: 0.8933 (m-80) cc_final: 0.8573 (m-80) REVERT: B 535 MET cc_start: 0.8174 (mpp) cc_final: 0.7885 (mmm) REVERT: C 173 TYR cc_start: 0.8531 (m-80) cc_final: 0.8300 (m-80) REVERT: C 191 TYR cc_start: 0.8988 (m-80) cc_final: 0.8655 (m-10) REVERT: C 347 ASN cc_start: 0.8933 (t0) cc_final: 0.8570 (t0) REVERT: D 530 MET cc_start: 0.6787 (mtp) cc_final: 0.6526 (ttt) REVERT: D 655 LYS cc_start: 0.8759 (tptp) cc_final: 0.7863 (pttt) REVERT: G 113 ASP cc_start: 0.8720 (t0) cc_final: 0.8142 (m-30) REVERT: G 166 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8289 (mtp85) REVERT: G 363 GLN cc_start: 0.8225 (mt0) cc_final: 0.7749 (mm-40) REVERT: G 446 SER cc_start: 0.9426 (t) cc_final: 0.9111 (p) REVERT: H 26 GLU cc_start: 0.7809 (tt0) cc_final: 0.7529 (tm-30) REVERT: H 33 GLU cc_start: 0.8450 (tt0) cc_final: 0.8081 (tt0) REVERT: H 43 GLN cc_start: 0.8961 (mp10) cc_final: 0.8571 (mp10) REVERT: L 14 SER cc_start: 0.7575 (t) cc_final: 0.7220 (p) REVERT: L 82 ASP cc_start: 0.7871 (m-30) cc_final: 0.7051 (t0) REVERT: E 43 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8723 (mp10) REVERT: E 74 ASP cc_start: 0.8607 (m-30) cc_final: 0.8331 (m-30) REVERT: E 100 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8496 (mt0) REVERT: J 14 SER cc_start: 0.7310 (OUTLIER) cc_final: 0.6738 (p) REVERT: J 42 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8022 (mt0) REVERT: F 26 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7362 (tm-30) REVERT: F 43 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8772 (mp10) REVERT: F 100 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8373 (mm-40) REVERT: K 37 GLN cc_start: 0.8563 (tt0) cc_final: 0.8049 (tt0) REVERT: K 82 ASP cc_start: 0.8209 (m-30) cc_final: 0.7300 (t0) outliers start: 31 outliers final: 26 residues processed: 355 average time/residue: 0.1590 time to fit residues: 84.0940 Evaluate side-chains 363 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 336 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 316 TRP Chi-restraints excluded: chain D residue 529 THR Chi-restraints excluded: chain G residue 72 HIS Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 294 ILE Chi-restraints excluded: chain G residue 316 TRP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 372 VAL Chi-restraints excluded: chain I residue 632 GLU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 96 GLU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain K residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 47 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 161 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106377 restraints weight = 30079.376| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.75 r_work: 0.3166 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20160 Z= 0.175 Angle : 0.687 8.586 27534 Z= 0.332 Chirality : 0.047 0.239 3318 Planarity : 0.004 0.057 3309 Dihedral : 7.558 57.606 4488 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.56 % Favored : 93.17 % Rotamer: Outliers : 1.73 % Allowed : 14.79 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 2256 helix: 1.42 (0.26), residues: 420 sheet: -0.09 (0.19), residues: 798 loop : -1.38 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 31 TYR 0.017 0.001 TYR D 638 PHE 0.018 0.002 PHE C 376 TRP 0.021 0.002 TRP G 427 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00409 (20025) covalent geometry : angle 0.65276 (27165) SS BOND : bond 0.00450 ( 36) SS BOND : angle 0.71399 ( 72) hydrogen bonds : bond 0.03421 ( 714) hydrogen bonds : angle 5.10194 ( 1890) link_ALPHA1-2 : bond 0.01492 ( 3) link_ALPHA1-2 : angle 5.29960 ( 9) link_ALPHA1-3 : bond 0.01003 ( 12) link_ALPHA1-3 : angle 1.61978 ( 36) link_ALPHA1-6 : bond 0.00501 ( 9) link_ALPHA1-6 : angle 1.59599 ( 27) link_BETA1-4 : bond 0.00762 ( 27) link_BETA1-4 : angle 2.32695 ( 81) link_NAG-ASN : bond 0.00331 ( 48) link_NAG-ASN : angle 1.92837 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4038.81 seconds wall clock time: 70 minutes 26.29 seconds (4226.29 seconds total)