Starting phenix.real_space_refine on Sat Jul 4 08:53:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rsn_24675/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_2026/7rsn_24675.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rsn_24675/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 10 Time building chain proxies: 3.44, per 1000 atoms: 0.18 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: 1.74 Conformation dependent library (CDL) restraints added in 592.9 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: 0.54 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: 3.18 Time building geometry restraints manager: 2.14 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 - 17.46: 10806 17.46 - 34.91: 294 34.91 - 52.37: 81 52.37 - 69.82: 38 69.82 - 87.28: 22 Dihedral angle restraints: 11241 sinusoidal: 4608 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 11238 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: 0.05 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: 0.980 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.350 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 : 10.530 87.277 6849 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/Z covalent geometry : bond 0.02274 / 1.21 (20025) covalent geometry : angle 1.84264 / 1.18 (27165) SS BOND : bond 0.01335 / 0.81 ( 36) SS BOND : angle 2.42274 / 1.68 ( 72) hydrogen bonds : bond 0.15149 / 10.27 ( 714) hydrogen bonds : angle 7.39503 / 5.21 ( 1890) link_ALPHA1-2 : bond 0.08233 / 4.13 ( 3) link_ALPHA1-2 : angle 5.70618 / 3.86 ( 9) link_ALPHA1-3 : bond 0.08932 / 5.22 ( 12) link_ALPHA1-3 : angle 4.69159 / 3.37 ( 36) link_ALPHA1-6 : bond 0.05787 / 3.11 ( 9) link_ALPHA1-6 : angle 2.64517 / 1.78 ( 27) link_BETA1-4 : bond 0.07664 / 4.89 ( 27) link_BETA1-4 : angle 5.29143 / 3.59 ( 81) link_NAG-ASN : bond 0.08162 / 5.13 ( 48) link_NAG-ASN : angle 2.35686 / 1.62 ( 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 : 0.628 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: 0.1458 time to fit residues: 133.7988 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 : 0.507 ------------------------------------------------------------------------------- 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... 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 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112656 restraints weight = 31155.784| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 3.24 r_work: 0.3254 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20160 Z= 0.193 Angle : 0.856 18.236 27534 Z= 0.416 Chirality : 0.049 0.371 3318 Planarity : 0.005 0.055 3309 Dihedral : 5.638 50.130 2475 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.99 % Favored : 95.74 % Rotamer: Outliers : 2.37 % Allowed : 8.23 % Favored : 89.40 % 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: 0.48 (0.18), residues: 2256 helix: 1.68 (0.28), residues: 381 sheet: 0.57 (0.18), residues: 762 loop : -0.27 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 444 TYR 0.017 0.002 TYR J 86 PHE 0.017 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/Z covalent geometry : bond 0.00423 / 0.19 (20025) covalent geometry : angle 0.80177 / 0.41 (27165) SS BOND : bond 0.00282 / 0.17 ( 36) SS BOND : angle 0.94689 / 0.64 ( 72) hydrogen bonds : bond 0.05342 / 3.65 ( 714) hydrogen bonds : angle 6.12556 / 4.35 ( 1890) link_ALPHA1-2 : bond 0.02025 / 1.01 ( 3) link_ALPHA1-2 : angle 4.37425 / 2.93 ( 9) link_ALPHA1-3 : bond 0.00847 / 0.45 ( 12) link_ALPHA1-3 : angle 1.75246 / 1.27 ( 36) link_ALPHA1-6 : bond 0.01075 / 0.60 ( 9) link_ALPHA1-6 : angle 1.45811 / 1.09 ( 27) link_BETA1-4 : bond 0.01229 / 0.82 ( 27) link_BETA1-4 : angle 3.63014 / 2.43 ( 81) link_NAG-ASN : bond 0.00779 / 0.43 ( 48) link_NAG-ASN : angle 2.95520 / 2.13 ( 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 434 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 386 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8753 (mtp85) cc_final: 0.8229 (ttm110) REVERT: A 177 TYR cc_start: 0.8811 (m-80) cc_final: 0.8542 (m-80) REVERT: A 191 TYR cc_start: 0.9084 (m-80) cc_final: 0.8846 (m-10) REVERT: A 217 TYR cc_start: 0.8841 (m-80) cc_final: 0.7100 (m-80) REVERT: A 293 GLU cc_start: 0.8531 (tt0) cc_final: 0.7790 (pp20) REVERT: A 429 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8303 (mp0) REVERT: B 535 MET cc_start: 0.8382 (mpp) cc_final: 0.7828 (mmm) REVERT: B 620 ASP cc_start: 0.6941 (p0) cc_final: 0.6550 (p0) REVERT: B 635 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6440 (mt) REVERT: B 654 GLU cc_start: 0.7702 (tp30) cc_final: 0.7459 (tp30) REVERT: C 113 ASP cc_start: 0.8431 (t70) cc_final: 0.8140 (m-30) REVERT: C 173 TYR cc_start: 0.8747 (m-80) cc_final: 0.8500 (m-80) REVERT: C 269 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7097 (mm-30) REVERT: C 293 GLU cc_start: 0.8533 (tt0) cc_final: 0.8062 (pp20) REVERT: C 316 TRP cc_start: 0.7247 (p90) cc_final: 0.6862 (p90) REVERT: C 502 LYS cc_start: 0.8256 (tttt) cc_final: 0.7708 (mttm) REVERT: G 83 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7579 (tp30) REVERT: G 166 ARG cc_start: 0.8987 (mtp85) cc_final: 0.8646 (mtm180) REVERT: G 293 GLU cc_start: 0.8333 (tt0) cc_final: 0.7685 (pp20) REVERT: G 315 ARG cc_start: 0.7061 (mmt180) cc_final: 0.6765 (mtm-85) REVERT: G 446 SER cc_start: 0.9240 (t) cc_final: 0.8942 (p) REVERT: I 603 ILE cc_start: 0.8180 (mp) cc_final: 0.7939 (mp) REVERT: H 65 GLN cc_start: 0.9001 (tt0) cc_final: 0.8680 (tp40) REVERT: L 42 GLN cc_start: 0.8331 (mm-40) cc_final: 0.7845 (mm-40) REVERT: J 42 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7878 (mm-40) REVERT: F 65 GLN cc_start: 0.8757 (tt0) cc_final: 0.8518 (tp40) REVERT: F 80 MET cc_start: 0.8806 (ttt) cc_final: 0.8483 (ttt) REVERT: F 96 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7772 (mtmm) REVERT: K 17 GLU cc_start: 0.8115 (tp30) cc_final: 0.7790 (tp30) REVERT: K 37 GLN cc_start: 0.8354 (tt0) cc_final: 0.8021 (tt0) outliers start: 48 outliers final: 26 residues processed: 414 average time/residue: 0.1484 time to fit residues: 92.7676 Evaluate side-chains 347 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 320 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 439 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 635 ILE 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 439 ILE 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 439 ILE 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 E residue 24 THR Chi-restraints excluded: chain E residue 53 THR 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: 4.9990 chunk 227 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 194 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 577 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 66 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109824 restraints weight = 30091.196| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.77 r_work: 0.3207 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20160 Z= 0.204 Angle : 0.762 17.268 27534 Z= 0.369 Chirality : 0.047 0.255 3318 Planarity : 0.005 0.056 3309 Dihedral : 5.302 46.217 2475 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.57 % Favored : 95.17 % Rotamer: Outliers : 2.76 % Allowed : 8.93 % Favored : 88.31 % 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: 0.13 (0.18), residues: 2256 helix: 1.69 (0.28), residues: 378 sheet: 0.23 (0.18), residues: 810 loop : -0.55 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 469 TYR 0.018 0.002 TYR J 86 PHE 0.022 0.002 PHE C 376 TRP 0.019 0.002 TRP F 50 HIS 0.004 0.002 HIS G 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (20025) covalent geometry : angle 0.72420 / 0.36 (27165) SS BOND : bond 0.00440 / 0.28 ( 36) SS BOND : angle 0.79721 / 0.56 ( 72) hydrogen bonds : bond 0.04238 / 2.89 ( 714) hydrogen bonds : angle 5.61388 / 4.00 ( 1890) link_ALPHA1-2 : bond 0.01818 / 0.91 ( 3) link_ALPHA1-2 : angle 4.73344 / 3.16 ( 9) link_ALPHA1-3 : bond 0.00618 / 0.33 ( 12) link_ALPHA1-3 : angle 1.52339 / 1.09 ( 36) link_ALPHA1-6 : bond 0.00794 / 0.45 ( 9) link_ALPHA1-6 : angle 1.47521 / 1.11 ( 27) link_BETA1-4 : bond 0.00838 / 0.58 ( 27) link_BETA1-4 : angle 2.79713 / 1.86 ( 81) link_NAG-ASN : bond 0.00503 / 0.29 ( 48) link_NAG-ASN : angle 2.20942 / 1.61 ( 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 438 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 382 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8737 (mtp85) cc_final: 0.8418 (mtp85) REVERT: A 191 TYR cc_start: 0.9029 (m-80) cc_final: 0.8806 (m-80) REVERT: A 217 TYR cc_start: 0.8912 (m-80) cc_final: 0.7443 (m-80) REVERT: A 323 ILE cc_start: 0.9477 (mm) cc_final: 0.9269 (mt) REVERT: B 603 ILE cc_start: 0.8574 (mp) cc_final: 0.8341 (mp) REVERT: B 635 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6661 (mt) REVERT: B 651 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7854 (t0) REVERT: C 173 TYR cc_start: 0.8659 (m-80) cc_final: 0.8411 (m-80) REVERT: C 191 TYR cc_start: 0.9009 (m-80) cc_final: 0.8508 (m-80) REVERT: C 316 TRP cc_start: 0.7404 (p90) cc_final: 0.7096 (p90) REVERT: C 502 LYS cc_start: 0.8328 (tttt) cc_final: 0.8092 (tttp) REVERT: G 166 ARG cc_start: 0.8900 (mtp85) cc_final: 0.8123 (mtm180) REVERT: G 446 SER cc_start: 0.9193 (t) cc_final: 0.8925 (p) REVERT: I 629 MET cc_start: 0.7765 (ttt) cc_final: 0.7511 (tpp) REVERT: I 651 ASN cc_start: 0.7918 (t0) cc_final: 0.7641 (t0) REVERT: H 38 ARG cc_start: 0.8738 (ttp-170) cc_final: 0.8528 (ttp80) REVERT: H 62 ASP cc_start: 0.8200 (m-30) cc_final: 0.7897 (t0) REVERT: H 100 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8261 (mt0) REVERT: L 42 GLN cc_start: 0.8227 (mm-40) cc_final: 0.7711 (mm-40) REVERT: E 62 ASP cc_start: 0.7983 (m-30) cc_final: 0.7648 (t0) REVERT: E 100 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8303 (mt0) REVERT: J 14 SER cc_start: 0.7379 (t) cc_final: 0.7079 (p) REVERT: J 42 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7646 (mm110) REVERT: F 26 GLU cc_start: 0.7446 (tm-30) cc_final: 0.7236 (tm-30) REVERT: F 62 ASP cc_start: 0.7997 (m-30) cc_final: 0.7647 (t0) REVERT: F 100 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8321 (mt0) REVERT: K 17 GLU cc_start: 0.8235 (tp30) cc_final: 0.7870 (tp30) REVERT: K 37 GLN cc_start: 0.8482 (tt0) cc_final: 0.7986 (tt0) outliers start: 56 outliers final: 40 residues processed: 407 average time/residue: 0.1419 time to fit residues: 87.7539 Evaluate side-chains 366 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 324 time to evaluate : 0.732 ------------------------------------------------------------------------------- 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 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 77 THR Chi-restraints excluded: chain C residue 198 THR 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 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 388 THR 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 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: 9.9990 chunk 172 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 207 optimal weight: 0.0040 chunk 98 optimal weight: 8.9990 chunk 184 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 377 ASN C 377 ASN G 377 ASN H 65 GLN K 6 GLN K 66 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110293 restraints weight = 30049.973| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.82 r_work: 0.3207 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20160 Z= 0.165 Angle : 0.698 13.974 27534 Z= 0.333 Chirality : 0.046 0.267 3318 Planarity : 0.005 0.063 3309 Dihedral : 5.093 41.450 2475 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.34 % Favored : 95.35 % Rotamer: Outliers : 2.71 % Allowed : 10.50 % Favored : 86.79 % 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: 0.01 (0.18), residues: 2256 helix: 1.82 (0.28), residues: 378 sheet: 0.10 (0.18), residues: 813 loop : -0.68 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 94 TYR 0.014 0.001 TYR F 98 PHE 0.018 0.002 PHE C 376 TRP 0.017 0.002 TRP H 50 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (20025) covalent geometry : angle 0.66269 / 0.33 (27165) SS BOND : bond 0.00312 / 0.21 ( 36) SS BOND : angle 0.74313 / 0.52 ( 72) hydrogen bonds : bond 0.03728 / 2.56 ( 714) hydrogen bonds : angle 5.37173 / 3.82 ( 1890) link_ALPHA1-2 : bond 0.01829 / 0.92 ( 3) link_ALPHA1-2 : angle 4.60424 / 3.07 ( 9) link_ALPHA1-3 : bond 0.00605 / 0.31 ( 12) link_ALPHA1-3 : angle 1.48274 / 1.06 ( 36) link_ALPHA1-6 : bond 0.00785 / 0.45 ( 9) link_ALPHA1-6 : angle 1.46047 / 1.08 ( 27) link_BETA1-4 : bond 0.00782 / 0.55 ( 27) link_BETA1-4 : angle 2.54173 / 1.69 ( 81) link_NAG-ASN : bond 0.00400 / 0.25 ( 48) link_NAG-ASN : angle 2.00809 / 1.49 ( 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 408 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 353 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: A 191 TYR cc_start: 0.8955 (m-80) cc_final: 0.8743 (m-80) REVERT: A 217 TYR cc_start: 0.8895 (m-80) cc_final: 0.7526 (m-80) REVERT: B 603 ILE cc_start: 0.8529 (mp) cc_final: 0.8295 (mp) REVERT: B 635 ILE cc_start: 0.7325 (OUTLIER) cc_final: 0.7090 (mt) REVERT: C 173 TYR cc_start: 0.8601 (m-80) cc_final: 0.8366 (m-80) REVERT: C 191 TYR cc_start: 0.9013 (m-80) cc_final: 0.8760 (m-80) REVERT: C 316 TRP cc_start: 0.7484 (p90) cc_final: 0.7097 (p90) REVERT: G 166 ARG cc_start: 0.8749 (mtp85) cc_final: 0.8265 (mtp85) REVERT: G 446 SER cc_start: 0.9305 (t) cc_final: 0.9000 (p) REVERT: I 615 SER cc_start: 0.6898 (t) cc_final: 0.6642 (p) REVERT: H 6 GLN cc_start: 0.8370 (mt0) cc_final: 0.8158 (tt0) REVERT: H 105 ARG cc_start: 0.8098 (mmt180) cc_final: 0.7880 (mmt180) REVERT: L 42 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7665 (mm-40) REVERT: E 62 ASP cc_start: 0.8024 (m-30) cc_final: 0.7791 (t0) REVERT: E 100 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8293 (mt0) REVERT: J 42 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7654 (mm110) REVERT: J 100 GLN cc_start: 0.8876 (mp10) cc_final: 0.8639 (mp10) REVERT: F 26 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7160 (tm-30) REVERT: F 62 ASP cc_start: 0.8005 (m-30) cc_final: 0.7782 (t0) REVERT: F 100 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8306 (mt0) REVERT: K 17 GLU cc_start: 0.8184 (tp30) cc_final: 0.7899 (tp30) REVERT: K 37 GLN cc_start: 0.8506 (tt0) cc_final: 0.7969 (tt0) outliers start: 55 outliers final: 35 residues processed: 383 average time/residue: 0.1513 time to fit residues: 88.1662 Evaluate side-chains 364 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 465 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 635 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 6 GLN 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 52 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 112 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 104 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 189 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 12 optimal weight: 0.0000 chunk 127 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN G 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108112 restraints weight = 30004.536| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.71 r_work: 0.3184 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20160 Z= 0.185 Angle : 0.696 12.951 27534 Z= 0.335 Chirality : 0.046 0.246 3318 Planarity : 0.005 0.061 3309 Dihedral : 4.990 37.677 2475 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.52 % Favored : 95.12 % Rotamer: Outliers : 2.61 % Allowed : 11.54 % Favored : 85.85 % 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: -0.12 (0.18), residues: 2256 helix: 1.68 (0.28), residues: 381 sheet: 0.12 (0.18), residues: 765 loop : -0.83 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 31 TYR 0.012 0.001 TYR I 638 PHE 0.019 0.002 PHE C 376 TRP 0.017 0.002 TRP F 50 HIS 0.004 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (20025) covalent geometry : angle 0.66252 / 0.33 (27165) SS BOND : bond 0.00640 / 0.46 ( 36) SS BOND : angle 0.67262 / 0.46 ( 72) hydrogen bonds : bond 0.03684 / 2.52 ( 714) hydrogen bonds : angle 5.28672 / 3.75 ( 1890) link_ALPHA1-2 : bond 0.01884 / 0.94 ( 3) link_ALPHA1-2 : angle 4.61347 / 3.07 ( 9) link_ALPHA1-3 : bond 0.00579 / 0.29 ( 12) link_ALPHA1-3 : angle 1.48332 / 1.07 ( 36) link_ALPHA1-6 : bond 0.00725 / 0.42 ( 9) link_ALPHA1-6 : angle 1.45379 / 1.07 ( 27) link_BETA1-4 : bond 0.00733 / 0.51 ( 27) link_BETA1-4 : angle 2.44558 / 1.62 ( 81) link_NAG-ASN : bond 0.00385 / 0.24 ( 48) link_NAG-ASN : angle 2.00379 / 1.45 ( 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 398 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.754 Fit side-chains REVERT: A 191 TYR cc_start: 0.8957 (m-80) cc_final: 0.8685 (m-80) REVERT: A 217 TYR cc_start: 0.8901 (m-80) cc_final: 0.7474 (m-80) REVERT: C 173 TYR cc_start: 0.8602 (m-80) cc_final: 0.8387 (m-80) REVERT: C 191 TYR cc_start: 0.9059 (m-80) cc_final: 0.8784 (m-80) REVERT: C 347 ASN cc_start: 0.8908 (t0) cc_final: 0.8582 (t0) REVERT: G 166 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8173 (mtp85) REVERT: G 446 SER cc_start: 0.9420 (t) cc_final: 0.9057 (p) REVERT: I 603 ILE cc_start: 0.8470 (mp) cc_final: 0.8123 (mp) REVERT: H 6 GLN cc_start: 0.8566 (mt0) cc_final: 0.8223 (tt0) REVERT: H 105 ARG cc_start: 0.8115 (mmt180) cc_final: 0.7900 (mmt180) REVERT: L 42 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7640 (mm-40) REVERT: E 94 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8561 (ttp-110) REVERT: E 100 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8358 (mt0) REVERT: J 42 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7640 (mm110) REVERT: F 26 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7223 (tm-30) REVERT: F 84 GLN cc_start: 0.8115 (tt0) cc_final: 0.7896 (tt0) REVERT: F 100 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8308 (mm-40) REVERT: K 17 GLU cc_start: 0.8291 (tp30) cc_final: 0.7988 (tp30) REVERT: K 37 GLN cc_start: 0.8548 (tt0) cc_final: 0.8050 (tt0) outliers start: 53 outliers final: 42 residues processed: 372 average time/residue: 0.1555 time to fit residues: 87.7103 Evaluate side-chains 362 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 320 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 C residue 38 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 388 THR 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 95 MET 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 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 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 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 104 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 35 optimal weight: 0.0970 chunk 164 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 590 GLN ** G 374 HIS ** 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 = 0.3626 r_free = 0.3626 target = 0.130721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.104842 restraints weight = 30100.003| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.76 r_work: 0.3146 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 20160 Z= 0.251 Angle : 0.752 11.593 27534 Z= 0.362 Chirality : 0.048 0.252 3318 Planarity : 0.005 0.062 3309 Dihedral : 5.135 34.309 2475 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 3.21 % Allowed : 12.18 % Favored : 84.62 % 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: -0.40 (0.18), residues: 2256 helix: 1.49 (0.27), residues: 399 sheet: -0.01 (0.19), residues: 774 loop : -1.11 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 107 TYR 0.015 0.002 TYR C 217 PHE 0.021 0.002 PHE C 376 TRP 0.018 0.002 TRP F 50 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (20025) covalent geometry : angle 0.71975 / 0.36 (27165) SS BOND : bond 0.00452 / 0.28 ( 36) SS BOND : angle 0.81826 / 0.56 ( 72) hydrogen bonds : bond 0.03991 / 2.72 ( 714) hydrogen bonds : angle 5.35391 / 3.78 ( 1890) link_ALPHA1-2 : bond 0.01750 / 0.88 ( 3) link_ALPHA1-2 : angle 4.72213 / 3.13 ( 9) link_ALPHA1-3 : bond 0.00553 / 0.28 ( 12) link_ALPHA1-3 : angle 1.49586 / 1.07 ( 36) link_ALPHA1-6 : bond 0.00684 / 0.39 ( 9) link_ALPHA1-6 : angle 1.49637 / 1.11 ( 27) link_BETA1-4 : bond 0.00727 / 0.51 ( 27) link_BETA1-4 : angle 2.44760 / 1.63 ( 81) link_NAG-ASN : bond 0.00371 / 0.23 ( 48) link_NAG-ASN : angle 2.07680 / 1.54 ( 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: 65 poor density : 340 time to evaluate : 0.702 Fit side-chains REVERT: A 191 TYR cc_start: 0.9070 (m-80) cc_final: 0.8778 (m-80) REVERT: B 603 ILE cc_start: 0.8611 (mp) cc_final: 0.8349 (mp) REVERT: C 97 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.8214 (mmm-85) REVERT: C 173 TYR cc_start: 0.8648 (m-80) cc_final: 0.8448 (m-80) REVERT: C 191 TYR cc_start: 0.9095 (m-80) cc_final: 0.8807 (m-10) REVERT: C 347 ASN cc_start: 0.8993 (t0) cc_final: 0.8653 (t0) REVERT: D 530 MET cc_start: 0.6931 (mtp) cc_final: 0.6532 (ttt) REVERT: D 601 LYS cc_start: 0.8091 (ptmm) cc_final: 0.7845 (ptmt) REVERT: D 655 LYS cc_start: 0.8858 (tptp) cc_final: 0.7851 (pttt) REVERT: G 166 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8501 (mtp85) REVERT: G 446 SER cc_start: 0.9481 (t) cc_final: 0.9157 (p) REVERT: H 26 GLU cc_start: 0.7999 (tt0) cc_final: 0.7572 (tm-30) REVERT: L 106 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8112 (mp) REVERT: F 26 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7471 (tm-30) REVERT: F 84 GLN cc_start: 0.8340 (tt0) cc_final: 0.8100 (tt0) REVERT: F 100 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8484 (mm-40) REVERT: K 37 GLN cc_start: 0.8676 (tt0) cc_final: 0.8136 (tt0) outliers start: 65 outliers final: 47 residues processed: 371 average time/residue: 0.1579 time to fit residues: 87.7808 Evaluate side-chains 371 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 316 TRP 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 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 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 6 GLN Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 106 ILE 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 J residue 78 MET 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 128 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 377 ASN 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 = 0.134190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108155 restraints weight = 30060.151| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.61 r_work: 0.3172 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5015 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= 0.144 Angle : 0.668 9.946 27534 Z= 0.320 Chirality : 0.045 0.241 3318 Planarity : 0.005 0.062 3309 Dihedral : 4.864 30.630 2475 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.01 % Favored : 94.73 % Rotamer: Outliers : 2.56 % Allowed : 12.43 % Favored : 85.01 % 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: -0.35 (0.18), residues: 2256 helix: 1.63 (0.27), residues: 402 sheet: -0.01 (0.19), residues: 768 loop : -1.11 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 94 TYR 0.014 0.001 TYR D 638 PHE 0.017 0.001 PHE C 376 TRP 0.018 0.002 TRP H 50 HIS 0.005 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (20025) covalent geometry : angle 0.63758 / 0.31 (27165) SS BOND : bond 0.00275 / 0.18 ( 36) SS BOND : angle 0.71437 / 0.49 ( 72) hydrogen bonds : bond 0.03364 / 2.28 ( 714) hydrogen bonds : angle 5.18240 / 3.66 ( 1890) link_ALPHA1-2 : bond 0.01954 / 0.98 ( 3) link_ALPHA1-2 : angle 4.60349 / 3.07 ( 9) link_ALPHA1-3 : bond 0.00647 / 0.32 ( 12) link_ALPHA1-3 : angle 1.43715 / 1.02 ( 36) link_ALPHA1-6 : bond 0.00672 / 0.39 ( 9) link_ALPHA1-6 : angle 1.42684 / 1.03 ( 27) link_BETA1-4 : bond 0.00744 / 0.52 ( 27) link_BETA1-4 : angle 2.26384 / 1.49 ( 81) link_NAG-ASN : bond 0.00336 / 0.22 ( 48) link_NAG-ASN : angle 1.83963 / 1.38 ( 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 406 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 354 time to evaluate : 0.752 Fit side-chains REVERT: A 191 TYR cc_start: 0.8915 (m-80) cc_final: 0.8604 (m-80) REVERT: B 603 ILE cc_start: 0.8569 (mp) cc_final: 0.8272 (mp) REVERT: B 660 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6797 (mm) REVERT: C 97 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.8068 (mmm-85) REVERT: C 112 TRP cc_start: 0.8381 (t-100) cc_final: 0.8168 (t-100) REVERT: C 173 TYR cc_start: 0.8541 (m-80) cc_final: 0.8318 (m-80) REVERT: C 191 TYR cc_start: 0.8973 (m-80) cc_final: 0.8713 (m-80) REVERT: C 347 ASN cc_start: 0.8926 (t0) cc_final: 0.8567 (t0) REVERT: C 502 LYS cc_start: 0.8074 (tttm) cc_final: 0.7062 (mtpt) REVERT: D 530 MET cc_start: 0.6703 (mtp) cc_final: 0.6384 (ttt) REVERT: D 601 LYS cc_start: 0.7877 (ptmm) cc_final: 0.7667 (ptmt) REVERT: D 620 ASP cc_start: 0.7078 (p0) cc_final: 0.6625 (p0) REVERT: D 655 LYS cc_start: 0.8771 (tptp) cc_final: 0.7837 (pttt) REVERT: G 166 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8075 (mtp85) REVERT: G 446 SER cc_start: 0.9395 (t) cc_final: 0.9066 (p) REVERT: I 603 ILE cc_start: 0.8723 (mp) cc_final: 0.8325 (mp) REVERT: H 26 GLU cc_start: 0.7716 (tt0) cc_final: 0.7434 (tm-30) REVERT: H 33 GLU cc_start: 0.8367 (tt0) cc_final: 0.7975 (tt0) REVERT: H 43 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8725 (mp10) REVERT: H 96 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8188 (mtmt) REVERT: L 42 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8076 (mm-40) REVERT: L 82 ASP cc_start: 0.7989 (m-30) cc_final: 0.6710 (t0) REVERT: L 106 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8086 (mp) REVERT: E 43 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8866 (mp10) REVERT: E 74 ASP cc_start: 0.8596 (m-30) cc_final: 0.8368 (m-30) REVERT: E 100 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8387 (mt0) REVERT: J 42 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7916 (mt0) REVERT: F 26 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7273 (tm-30) REVERT: F 43 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8754 (mm-40) REVERT: F 84 GLN cc_start: 0.8060 (tt0) cc_final: 0.7832 (tt0) REVERT: F 100 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8344 (mm-40) REVERT: K 37 GLN cc_start: 0.8568 (tt0) cc_final: 0.8039 (tt0) outliers start: 52 outliers final: 42 residues processed: 379 average time/residue: 0.1607 time to fit residues: 91.6465 Evaluate side-chains 385 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 B residue 529 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL 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 D residue 529 THR Chi-restraints excluded: chain G residue 38 VAL 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 I residue 648 GLU 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 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE 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 E residue 112 SER Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 65 SER Chi-restraints excluded: chain J residue 78 MET 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 K residue 96 GLU 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: 5.9990 chunk 45 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 218 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.106682 restraints weight = 30209.493| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.64 r_work: 0.3151 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20160 Z= 0.174 Angle : 0.681 8.984 27534 Z= 0.327 Chirality : 0.046 0.240 3318 Planarity : 0.004 0.060 3309 Dihedral : 4.831 29.442 2475 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.54 % Favored : 94.19 % Rotamer: Outliers : 2.61 % Allowed : 12.62 % Favored : 84.76 % 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: -0.39 (0.18), residues: 2256 helix: 1.63 (0.27), residues: 402 sheet: -0.03 (0.19), residues: 762 loop : -1.14 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 82A TYR 0.022 0.001 TYR B 638 PHE 0.018 0.002 PHE C 376 TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (20025) covalent geometry : angle 0.65050 / 0.32 (27165) SS BOND : bond 0.00450 / 0.26 ( 36) SS BOND : angle 0.69740 / 0.48 ( 72) hydrogen bonds : bond 0.03456 / 2.35 ( 714) hydrogen bonds : angle 5.14938 / 3.63 ( 1890) link_ALPHA1-2 : bond 0.01806 / 0.91 ( 3) link_ALPHA1-2 : angle 4.63366 / 3.08 ( 9) link_ALPHA1-3 : bond 0.00592 / 0.30 ( 12) link_ALPHA1-3 : angle 1.45598 / 1.04 ( 36) link_ALPHA1-6 : bond 0.00645 / 0.37 ( 9) link_ALPHA1-6 : angle 1.51095 / 1.09 ( 27) link_BETA1-4 : bond 0.00729 / 0.52 ( 27) link_BETA1-4 : angle 2.29827 / 1.52 ( 81) link_NAG-ASN : bond 0.00307 / 0.20 ( 48) link_NAG-ASN : angle 1.82349 / 1.35 ( 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 398 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 345 time to evaluate : 0.766 Fit side-chains REVERT: A 113 ASP cc_start: 0.8626 (m-30) cc_final: 0.8392 (m-30) REVERT: A 191 TYR cc_start: 0.8938 (m-80) cc_final: 0.8532 (m-10) REVERT: B 603 ILE cc_start: 0.8455 (mp) cc_final: 0.8188 (mp) REVERT: B 660 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7021 (mm) REVERT: C 173 TYR cc_start: 0.8575 (m-80) cc_final: 0.8353 (m-80) REVERT: C 191 TYR cc_start: 0.8981 (m-80) cc_final: 0.8724 (m-80) REVERT: C 347 ASN cc_start: 0.8960 (t0) cc_final: 0.8571 (t0) REVERT: C 502 LYS cc_start: 0.8064 (tttm) cc_final: 0.7048 (mtpt) REVERT: D 530 MET cc_start: 0.6617 (mtp) cc_final: 0.6342 (ttt) REVERT: D 655 LYS cc_start: 0.8754 (tptp) cc_final: 0.7904 (pttt) REVERT: G 166 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8338 (mtp85) REVERT: G 446 SER cc_start: 0.9401 (t) cc_final: 0.9092 (p) REVERT: I 635 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7700 (mt) REVERT: H 6 GLN cc_start: 0.8622 (mt0) cc_final: 0.8397 (tt0) REVERT: H 26 GLU cc_start: 0.7774 (tt0) cc_final: 0.7467 (tm-30) REVERT: H 33 GLU cc_start: 0.8472 (tt0) cc_final: 0.8097 (tt0) REVERT: H 43 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8612 (mp10) REVERT: H 65 GLN cc_start: 0.8757 (tp40) cc_final: 0.8542 (mm-40) REVERT: H 96 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8202 (mtmt) REVERT: L 106 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8065 (mp) REVERT: E 43 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8800 (mp10) REVERT: E 74 ASP cc_start: 0.8639 (m-30) cc_final: 0.8375 (m-30) REVERT: E 100 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8447 (mt0) REVERT: J 42 GLN cc_start: 0.8332 (mm-40) cc_final: 0.7952 (mt0) REVERT: F 26 GLU cc_start: 0.7619 (tm-30) cc_final: 0.7286 (tm-30) REVERT: F 43 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8727 (mm-40) REVERT: F 100 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8417 (mm-40) REVERT: K 37 GLN cc_start: 0.8638 (tt0) cc_final: 0.8123 (tt0) outliers start: 53 outliers final: 45 residues processed: 371 average time/residue: 0.1545 time to fit residues: 86.2166 Evaluate side-chains 379 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 660 LEU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG 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 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 632 GLU Chi-restraints excluded: chain I residue 635 ILE Chi-restraints excluded: chain I residue 648 GLU 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 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 18 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 106 ILE 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 E residue 112 SER 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 K residue 96 GLU 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: 0.0870 chunk 70 optimal weight: 0.9990 chunk 184 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107429 restraints weight = 29911.014| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.63 r_work: 0.3165 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20160 Z= 0.159 Angle : 0.666 10.286 27534 Z= 0.319 Chirality : 0.045 0.239 3318 Planarity : 0.004 0.058 3309 Dihedral : 4.736 28.110 2475 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.41 % Favored : 94.33 % Rotamer: Outliers : 2.47 % Allowed : 12.87 % Favored : 84.66 % 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: -0.42 (0.18), residues: 2256 helix: 1.42 (0.26), residues: 420 sheet: -0.02 (0.19), residues: 762 loop : -1.14 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 94 TYR 0.028 0.001 TYR B 638 PHE 0.017 0.001 PHE C 376 TRP 0.025 0.002 TRP I 614 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (20025) covalent geometry : angle 0.63616 / 0.31 (27165) SS BOND : bond 0.00371 / 0.23 ( 36) SS BOND : angle 0.69362 / 0.48 ( 72) hydrogen bonds : bond 0.03336 / 2.25 ( 714) hydrogen bonds : angle 5.09129 / 3.60 ( 1890) link_ALPHA1-2 : bond 0.01883 / 0.94 ( 3) link_ALPHA1-2 : angle 4.54936 / 3.03 ( 9) link_ALPHA1-3 : bond 0.00628 / 0.31 ( 12) link_ALPHA1-3 : angle 1.43724 / 1.02 ( 36) link_ALPHA1-6 : bond 0.00641 / 0.37 ( 9) link_ALPHA1-6 : angle 1.44582 / 1.05 ( 27) link_BETA1-4 : bond 0.00722 / 0.51 ( 27) link_BETA1-4 : angle 2.23389 / 1.47 ( 81) link_NAG-ASN : bond 0.00311 / 0.20 ( 48) link_NAG-ASN : angle 1.78017 / 1.32 ( 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 390 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.772 Fit side-chains REVERT: A 113 ASP cc_start: 0.8654 (m-30) cc_final: 0.8410 (m-30) REVERT: A 191 TYR cc_start: 0.8927 (m-80) cc_final: 0.8523 (m-10) REVERT: B 660 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7015 (mm) REVERT: C 113 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8139 (m-30) REVERT: C 173 TYR cc_start: 0.8562 (m-80) cc_final: 0.8336 (m-80) REVERT: C 191 TYR cc_start: 0.8970 (m-80) cc_final: 0.8709 (m-80) REVERT: C 347 ASN cc_start: 0.8955 (t0) cc_final: 0.8548 (t0) REVERT: C 502 LYS cc_start: 0.8062 (tttm) cc_final: 0.7050 (mtpt) REVERT: D 530 MET cc_start: 0.6586 (mtp) cc_final: 0.6344 (ttt) REVERT: D 655 LYS cc_start: 0.8767 (tptp) cc_final: 0.7910 (pttt) REVERT: G 166 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8179 (mtp85) REVERT: G 446 SER cc_start: 0.9395 (t) cc_final: 0.9100 (p) REVERT: H 6 GLN cc_start: 0.8671 (mt0) cc_final: 0.8431 (tt0) REVERT: H 26 GLU cc_start: 0.7789 (tt0) cc_final: 0.7510 (tm-30) REVERT: H 33 GLU cc_start: 0.8448 (tt0) cc_final: 0.8094 (tt0) REVERT: H 43 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8635 (mp10) REVERT: H 65 GLN cc_start: 0.8840 (tp40) cc_final: 0.8618 (mm-40) REVERT: L 54 ARG cc_start: 0.8512 (ptp-110) cc_final: 0.8283 (ptp-110) REVERT: L 82 ASP cc_start: 0.7925 (m-30) cc_final: 0.6780 (t0) REVERT: L 106 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8040 (mp) REVERT: E 43 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8815 (mp10) REVERT: E 74 ASP cc_start: 0.8582 (m-30) cc_final: 0.8309 (m-30) REVERT: E 100 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8463 (mt0) REVERT: J 42 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7963 (mt0) REVERT: F 26 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7302 (tm-30) REVERT: F 84 GLN cc_start: 0.8034 (tt0) cc_final: 0.7815 (tt0) REVERT: F 100 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8382 (mm-40) REVERT: K 37 GLN cc_start: 0.8636 (tt0) cc_final: 0.8117 (tt0) outliers start: 50 outliers final: 44 residues processed: 368 average time/residue: 0.1485 time to fit residues: 81.9058 Evaluate side-chains 374 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 327 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 611 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG 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 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 323 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 I residue 648 GLU 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 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 L residue 106 ILE 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 E residue 112 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 52 VAL Chi-restraints excluded: chain F residue 53 THR 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: 5.9990 chunk 39 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 0.0040 chunk 179 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 258 GLN C 363 GLN ** G 374 HIS ** 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 = 0.3644 r_free = 0.3644 target = 0.131986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105910 restraints weight = 30227.991| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.78 r_work: 0.3168 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20160 Z= 0.203 Angle : 0.698 8.892 27534 Z= 0.336 Chirality : 0.046 0.241 3318 Planarity : 0.004 0.057 3309 Dihedral : 4.813 28.355 2475 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.12 % Favored : 93.66 % Rotamer: Outliers : 2.47 % Allowed : 12.97 % Favored : 84.57 % 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: -0.49 (0.18), residues: 2256 helix: 1.38 (0.26), residues: 420 sheet: -0.07 (0.19), residues: 762 loop : -1.19 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 31 TYR 0.049 0.002 TYR I 638 PHE 0.019 0.002 PHE C 376 TRP 0.017 0.002 TRP F 50 HIS 0.005 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (20025) covalent geometry : angle 0.66840 / 0.33 (27165) SS BOND : bond 0.00457 / 0.30 ( 36) SS BOND : angle 0.72311 / 0.50 ( 72) hydrogen bonds : bond 0.03535 / 2.39 ( 714) hydrogen bonds : angle 5.14838 / 3.64 ( 1890) link_ALPHA1-2 : bond 0.01816 / 0.91 ( 3) link_ALPHA1-2 : angle 4.57113 / 3.03 ( 9) link_ALPHA1-3 : bond 0.00599 / 0.30 ( 12) link_ALPHA1-3 : angle 1.44810 / 1.03 ( 36) link_ALPHA1-6 : bond 0.00607 / 0.35 ( 9) link_ALPHA1-6 : angle 1.47028 / 1.07 ( 27) link_BETA1-4 : bond 0.00701 / 0.49 ( 27) link_BETA1-4 : angle 2.27155 / 1.50 ( 81) link_NAG-ASN : bond 0.00303 / 0.20 ( 48) link_NAG-ASN : angle 1.84040 / 1.36 ( 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 377 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 327 time to evaluate : 0.798 Fit side-chains REVERT: A 113 ASP cc_start: 0.8659 (m-30) cc_final: 0.8441 (m-30) REVERT: A 191 TYR cc_start: 0.8911 (m-80) cc_final: 0.8530 (m-10) REVERT: B 660 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7016 (mm) REVERT: C 113 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8150 (m-30) REVERT: C 173 TYR cc_start: 0.8584 (m-80) cc_final: 0.8359 (m-80) REVERT: C 191 TYR cc_start: 0.8956 (m-80) cc_final: 0.8634 (m-10) REVERT: C 347 ASN cc_start: 0.8950 (t0) cc_final: 0.8538 (t0) REVERT: C 502 LYS cc_start: 0.8081 (tttm) cc_final: 0.7055 (mtpt) REVERT: D 530 MET cc_start: 0.6674 (mtp) cc_final: 0.6440 (ttt) REVERT: D 655 LYS cc_start: 0.8775 (tptp) cc_final: 0.7915 (pttt) REVERT: G 166 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8299 (mtp85) REVERT: G 446 SER cc_start: 0.9379 (t) cc_final: 0.9120 (p) REVERT: I 530 MET cc_start: 0.6596 (mtp) cc_final: 0.5913 (ttt) REVERT: H 6 GLN cc_start: 0.8670 (mt0) cc_final: 0.8453 (tt0) REVERT: H 26 GLU cc_start: 0.7832 (tt0) cc_final: 0.7537 (tm-30) REVERT: H 33 GLU cc_start: 0.8432 (tt0) cc_final: 0.8061 (tt0) REVERT: H 43 GLN cc_start: 0.9029 (mm-40) cc_final: 0.8630 (mp10) REVERT: H 65 GLN cc_start: 0.8838 (tp40) cc_final: 0.8622 (mm-40) REVERT: L 54 ARG cc_start: 0.8585 (ptp-110) cc_final: 0.8358 (ptp-110) REVERT: L 82 ASP cc_start: 0.7924 (m-30) cc_final: 0.6790 (t0) REVERT: L 106 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (mp) REVERT: E 43 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8744 (mp10) REVERT: E 100 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8486 (mt0) REVERT: J 42 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7983 (mt0) REVERT: F 26 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7332 (tm-30) REVERT: F 84 GLN cc_start: 0.8110 (tt0) cc_final: 0.7907 (tt0) REVERT: F 100 GLN cc_start: 0.8680 (mm-40) cc_final: 0.8398 (mm-40) REVERT: K 37 GLN cc_start: 0.8634 (tt0) cc_final: 0.8115 (tt0) outliers start: 50 outliers final: 45 residues processed: 356 average time/residue: 0.1598 time to fit residues: 85.5251 Evaluate side-chains 370 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 660 LEU Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 66 ARG 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 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 323 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 I residue 648 GLU 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 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 L residue 106 ILE 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 E residue 112 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 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 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 47 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 HIS ** 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 = 0.3627 r_free = 0.3627 target = 0.130653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.104448 restraints weight = 30350.487| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.78 r_work: 0.3141 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 20160 Z= 0.235 Angle : 0.727 8.955 27534 Z= 0.352 Chirality : 0.047 0.248 3318 Planarity : 0.004 0.055 3309 Dihedral : 4.948 28.088 2475 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.34 % Favored : 93.44 % Rotamer: Outliers : 2.47 % Allowed : 13.17 % Favored : 84.37 % 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: -0.61 (0.18), residues: 2256 helix: 1.33 (0.26), residues: 420 sheet: -0.15 (0.19), residues: 771 loop : -1.30 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 31 TYR 0.025 0.002 TYR B 638 PHE 0.022 0.002 PHE C 376 TRP 0.033 0.002 TRP A 69 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (20025) covalent geometry : angle 0.69781 / 0.35 (27165) SS BOND : bond 0.00477 / 0.30 ( 36) SS BOND : angle 0.77618 / 0.54 ( 72) hydrogen bonds : bond 0.03765 / 2.56 ( 714) hydrogen bonds : angle 5.25095 / 3.71 ( 1890) link_ALPHA1-2 : bond 0.01812 / 0.91 ( 3) link_ALPHA1-2 : angle 4.64457 / 3.07 ( 9) link_ALPHA1-3 : bond 0.00604 / 0.30 ( 12) link_ALPHA1-3 : angle 1.46428 / 1.04 ( 36) link_ALPHA1-6 : bond 0.00594 / 0.35 ( 9) link_ALPHA1-6 : angle 1.47448 / 1.07 ( 27) link_BETA1-4 : bond 0.00690 / 0.49 ( 27) link_BETA1-4 : angle 2.29863 / 1.52 ( 81) link_NAG-ASN : bond 0.00316 / 0.20 ( 48) link_NAG-ASN : angle 1.93603 / 1.42 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4251.64 seconds wall clock time: 73 minutes 58.43 seconds (4438.43 seconds total)