Starting phenix.real_space_refine on Sat Jun 6 01:28:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.map" model { file = "/net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6e_71307/06_2026/9p6e_71307.cif" } resolution = 2.7 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= -0.000 sd= 0.043 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 150 5.16 5 C 15444 2.51 5 N 4206 2.21 5 O 4878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24678 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3429 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1061 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "L" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 706 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "C" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3429 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "K" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1061 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "N" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 706 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "E" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3429 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "O" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "Q" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 803 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "P" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1061 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "R" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 706 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.25, per 1000 atoms: 0.25 Number of scatterers: 24678 At special positions: 0 Unit cell: (139.576, 138.543, 146.814, 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 150 16.00 O 4878 8.00 N 4206 7.00 C 15444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.05 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA W 3 " - " MAN W 5 " " BMA a 3 " - " MAN a 5 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " 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 Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 88 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 295 " " NAG A 607 " - " ASN A 156 " " NAG A 608 " - " ASN A 197 " " NAG A 609 " - " ASN A 448 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 160 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 88 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 156 " " NAG C 608 " - " ASN C 197 " " NAG C 609 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 88 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 295 " " NAG E 607 " - " ASN E 156 " " NAG E 608 " - " ASN E 197 " " NAG E 609 " - " ASN E 448 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 637 " " NAG S 1 " - " ASN A 276 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 392 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 386 " " NAG c 1 " - " ASN E 392 " " NAG d 1 " - " ASN E 262 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 1.5 seconds 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 18.8% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.917A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.931A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.636A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.693A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.472A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 3.666A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.547A pdb=" N ASP I 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 79 through 83' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 60 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.754A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.917A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.930A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.636A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.693A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.473A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.666A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 596 Processing helix chain 'D' and resid 618 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.547A pdb=" N ASP M 82 " --> pdb=" O GLN M 79 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 79 through 83' Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.755A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.917A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.930A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 390 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.636A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 425 through 429' Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.693A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.473A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.666A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 596 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'Q' and resid 79 through 83 removed outlier: 3.547A pdb=" N ASP Q 82 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLU Q 83 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 79 through 83' Processing helix chain 'P' and resid 28 through 30 No H-bonds generated for 'chain 'P' and resid 28 through 30' Processing helix chain 'P' and resid 60 through 64 Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.755A pdb=" N THR P 87 " --> pdb=" O SER P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.545A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.214A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.399A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.776A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'G' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 11 current: chain 'G' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'I' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 12 current: chain 'I' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 48 current: chain 'I' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.579A pdb=" N LEU H 82C" --> pdb=" O GLY H 15 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER H 17 " --> pdb=" O ARG H 82A" (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG H 82A" --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG H 19 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP H 81 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER H 21 " --> pdb=" O PHE H 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE H 79 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU H 23 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR H 77 " --> pdb=" O GLU H 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 58 current: chain 'H' and resid 100K through 103 Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 24 Processing sheet with id=AB6, first strand: chain 'L' and resid 34 through 38 removed outlier: 6.627A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.545A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.214A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 6.776A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323A current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC5, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'J' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 11 current: chain 'J' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'M' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 9 through 12 current: chain 'M' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 96 through 98 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AC9, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.579A pdb=" N LEU K 82C" --> pdb=" O GLY K 15 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER K 17 " --> pdb=" O ARG K 82A" (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG K 82A" --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG K 19 " --> pdb=" O ASP K 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP K 81 " --> pdb=" O ARG K 19 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER K 21 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE K 79 " --> pdb=" O SER K 21 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU K 23 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR K 77 " --> pdb=" O GLU K 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 10 through 12 current: chain 'K' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 58 current: chain 'K' and resid 100K through 103 Processing sheet with id=AD2, first strand: chain 'N' and resid 18 through 24 Processing sheet with id=AD3, first strand: chain 'N' and resid 34 through 38 removed outlier: 6.627A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 97 through 98 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.545A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.214A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.776A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AE2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'O' and resid 10 through 11 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 10 through 11 current: chain 'O' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 96 through 98 No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE6, first strand: chain 'P' and resid 3 through 6 removed outlier: 3.579A pdb=" N LEU P 82C" --> pdb=" O GLY P 15 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER P 17 " --> pdb=" O ARG P 82A" (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG P 82A" --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG P 19 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP P 81 " --> pdb=" O ARG P 19 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER P 21 " --> pdb=" O PHE P 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE P 79 " --> pdb=" O SER P 21 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU P 23 " --> pdb=" O THR P 77 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR P 77 " --> pdb=" O GLU P 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 10 through 12 current: chain 'P' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 58 current: chain 'P' and resid 100K through 103 Processing sheet with id=AE8, first strand: chain 'R' and resid 18 through 24 Processing sheet with id=AE9, first strand: chain 'R' and resid 34 through 38 removed outlier: 6.627A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 654 hydrogen bonds defined for protein. 1710 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: 4.62 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7923 1.35 - 1.48: 6755 1.48 - 1.62: 10318 1.62 - 1.75: 3 1.75 - 1.89: 204 Bond restraints: 25203 Sorted by residual: bond pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " ideal model delta sigma weight residual 1.808 1.886 -0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" CB CYS E 74 " pdb=" SG CYS E 74 " ideal model delta sigma weight residual 1.808 1.886 -0.078 3.30e-02 9.18e+02 5.64e+00 bond pdb=" CB CYS C 74 " pdb=" SG CYS C 74 " ideal model delta sigma weight residual 1.808 1.886 -0.078 3.30e-02 9.18e+02 5.61e+00 bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.48e+00 bond pdb=" C THR E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.44e+00 ... (remaining 25198 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 33509 2.79 - 5.58: 628 5.58 - 8.36: 51 8.36 - 11.15: 3 11.15 - 13.94: 3 Bond angle restraints: 34194 Sorted by residual: angle pdb=" CA CYS E 54 " pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " ideal model delta sigma weight residual 114.40 128.34 -13.94 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " ideal model delta sigma weight residual 114.40 128.33 -13.93 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " ideal model delta sigma weight residual 114.40 128.30 -13.90 2.30e+00 1.89e-01 3.65e+01 angle pdb=" C CYS A 54 " pdb=" CA CYS A 54 " pdb=" CB CYS A 54 " ideal model delta sigma weight residual 109.80 101.50 8.30 1.65e+00 3.67e-01 2.53e+01 angle pdb=" C CYS C 54 " pdb=" CA CYS C 54 " pdb=" CB CYS C 54 " ideal model delta sigma weight residual 109.80 101.51 8.29 1.65e+00 3.67e-01 2.52e+01 ... (remaining 34189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.79: 14877 20.79 - 41.58: 684 41.58 - 62.37: 207 62.37 - 83.15: 66 83.15 - 103.94: 36 Dihedral angle restraints: 15870 sinusoidal: 7185 harmonic: 8685 Sorted by residual: dihedral pdb=" CD ARG K 71 " pdb=" NE ARG K 71 " pdb=" CZ ARG K 71 " pdb=" NH1 ARG K 71 " ideal model delta sinusoidal sigma weight residual 0.00 -70.52 70.52 1 1.00e+01 1.00e-02 6.40e+01 dihedral pdb=" CD ARG H 71 " pdb=" NE ARG H 71 " pdb=" CZ ARG H 71 " pdb=" NH1 ARG H 71 " ideal model delta sinusoidal sigma weight residual 0.00 -70.45 70.45 1 1.00e+01 1.00e-02 6.39e+01 dihedral pdb=" CD ARG P 71 " pdb=" NE ARG P 71 " pdb=" CZ ARG P 71 " pdb=" NH1 ARG P 71 " ideal model delta sinusoidal sigma weight residual 0.00 -70.43 70.43 1 1.00e+01 1.00e-02 6.39e+01 ... (remaining 15867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3338 0.080 - 0.160: 595 0.160 - 0.240: 14 0.240 - 0.320: 1 0.320 - 0.401: 6 Chirality restraints: 3954 Sorted by residual: chirality pdb=" C1 NAG E 608 " pdb=" ND2 ASN E 197 " pdb=" C2 NAG E 608 " pdb=" O5 NAG E 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG A 608 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG A 608 " pdb=" O5 NAG A 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 276 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 3951 not shown) Planarity restraints: 4350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 71 " 0.904 9.50e-02 1.11e+02 4.06e-01 1.08e+02 pdb=" NE ARG K 71 " -0.072 2.00e-02 2.50e+03 pdb=" CZ ARG K 71 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG K 71 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG K 71 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 71 " 0.904 9.50e-02 1.11e+02 4.06e-01 1.08e+02 pdb=" NE ARG P 71 " -0.072 2.00e-02 2.50e+03 pdb=" CZ ARG P 71 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG P 71 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG P 71 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 71 " -0.904 9.50e-02 1.11e+02 4.06e-01 1.08e+02 pdb=" NE ARG H 71 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG H 71 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG H 71 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG H 71 " -0.005 2.00e-02 2.50e+03 ... (remaining 4347 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3329 2.76 - 3.30: 22108 3.30 - 3.83: 41818 3.83 - 4.37: 52373 4.37 - 4.90: 87877 Nonbonded interactions: 207505 Sorted by model distance: nonbonded pdb=" O GLY P 65 " pdb=" NH2 ARG P 82A" model vdw 2.230 3.120 nonbonded pdb=" O GLY H 65 " pdb=" NH2 ARG H 82A" model vdw 2.230 3.120 nonbonded pdb=" O GLY K 65 " pdb=" NH2 ARG K 82A" model vdw 2.230 3.120 nonbonded pdb=" OD1 ASP N 83 " pdb=" NZ LYS N 103 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP L 83 " pdb=" NZ LYS L 103 " model vdw 2.258 3.120 ... (remaining 207500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'W' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' 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: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.090 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 25314 Z= 0.224 Angle : 0.947 13.938 34485 Z= 0.499 Chirality : 0.058 0.401 3954 Planarity : 0.017 0.406 4305 Dihedral : 14.645 103.942 10188 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 0.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Rotamer: Outliers : 0.92 % Allowed : 9.62 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.15), residues: 2988 helix: 0.62 (0.26), residues: 402 sheet: 0.67 (0.16), residues: 1002 loop : 0.14 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.003 ARG A 192 TYR 0.023 0.003 TYR C 191 PHE 0.029 0.003 PHE A 53 TRP 0.021 0.002 TRP K 47 HIS 0.009 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.22 (25203) covalent geometry : angle 0.93198 / 0.50 (34194) SS BOND : bond 0.00847 / 0.48 ( 42) SS BOND : angle 1.96558 / 1.32 ( 84) hydrogen bonds : bond 0.14013 / 9.50 ( 654) hydrogen bonds : angle 7.02098 / 4.80 ( 1710) link_ALPHA1-3 : bond 0.00213 / 0.11 ( 3) link_ALPHA1-3 : angle 1.58239 / 1.04 ( 9) link_ALPHA1-6 : bond 0.00435 / 0.22 ( 3) link_ALPHA1-6 : angle 1.44282 / 1.00 ( 9) link_BETA1-4 : bond 0.00327 / 0.22 ( 18) link_BETA1-4 : angle 2.24760 / 1.54 ( 54) link_NAG-ASN : bond 0.00300 / 0.19 ( 45) link_NAG-ASN : angle 2.13027 / 1.45 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 476 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8758 (tp30) cc_final: 0.8315 (tp30) REVERT: A 121 LYS cc_start: 0.8761 (mttt) cc_final: 0.8555 (tptt) REVERT: A 137 ASN cc_start: 0.6620 (m-40) cc_final: 0.6275 (m-40) REVERT: A 153 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7129 (mt-10) REVERT: A 189 LYS cc_start: 0.7379 (mttt) cc_final: 0.6639 (tttm) REVERT: A 211 GLU cc_start: 0.8147 (tt0) cc_final: 0.7788 (tp30) REVERT: A 308 ARG cc_start: 0.8368 (mmt-90) cc_final: 0.8032 (mmm-85) REVERT: A 315 GLN cc_start: 0.7561 (mt0) cc_final: 0.7337 (mm110) REVERT: A 335 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7925 (tttm) REVERT: A 504 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7652 (tpm170) REVERT: B 620 SER cc_start: 0.9079 (p) cc_final: 0.8694 (t) REVERT: B 659 ASP cc_start: 0.8768 (m-30) cc_final: 0.8518 (m-30) REVERT: I 86 TYR cc_start: 0.8103 (m-80) cc_final: 0.7890 (m-80) REVERT: I 87 TYR cc_start: 0.8479 (m-80) cc_final: 0.8106 (m-80) REVERT: I 96 TYR cc_start: 0.8981 (m-80) cc_final: 0.8637 (m-80) REVERT: H 51 MET cc_start: 0.8967 (tmm) cc_final: 0.8722 (tmm) REVERT: H 71 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7019 (ptt90) REVERT: H 74 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8080 (t) REVERT: H 75 GLN cc_start: 0.8021 (mt0) cc_final: 0.7499 (mp10) REVERT: H 100 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7906 (mmmt) REVERT: H 105 ARG cc_start: 0.8033 (mmt180) cc_final: 0.7703 (mmt180) REVERT: C 92 GLU cc_start: 0.8755 (tp30) cc_final: 0.8517 (tp30) REVERT: C 121 LYS cc_start: 0.8739 (mttt) cc_final: 0.8438 (mmtt) REVERT: C 137 ASN cc_start: 0.6490 (m-40) cc_final: 0.6093 (m-40) REVERT: C 189 LYS cc_start: 0.7586 (mttt) cc_final: 0.6779 (tttm) REVERT: C 211 GLU cc_start: 0.8293 (tt0) cc_final: 0.7785 (tp30) REVERT: C 327 ARG cc_start: 0.7593 (mpp-170) cc_final: 0.7333 (mtm110) REVERT: C 335 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7962 (ttpp) REVERT: C 475 MET cc_start: 0.8850 (mmp) cc_final: 0.8328 (tpp) REVERT: C 479 TRP cc_start: 0.7743 (m-10) cc_final: 0.5791 (m-10) REVERT: D 659 ASP cc_start: 0.8740 (m-30) cc_final: 0.8533 (m-30) REVERT: J 34 MET cc_start: 0.8817 (mmm) cc_final: 0.8513 (mmt) REVERT: J 46 GLU cc_start: 0.8716 (tt0) cc_final: 0.8292 (tt0) REVERT: J 91 TYR cc_start: 0.8425 (m-80) cc_final: 0.7899 (m-80) REVERT: M 50 ASP cc_start: 0.8161 (m-30) cc_final: 0.7838 (m-30) REVERT: M 53 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8480 (mm-40) REVERT: K 48 MET cc_start: 0.9208 (mtp) cc_final: 0.8992 (mtm) REVERT: K 53 MET cc_start: 0.8556 (tpt) cc_final: 0.8306 (tpp) REVERT: K 75 GLN cc_start: 0.8090 (mt0) cc_final: 0.7444 (mp-120) REVERT: K 91 TYR cc_start: 0.8640 (m-80) cc_final: 0.8358 (m-80) REVERT: K 100 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8129 (mmmt) REVERT: E 92 GLU cc_start: 0.8740 (tp30) cc_final: 0.8463 (tp30) REVERT: E 121 LYS cc_start: 0.8833 (mttt) cc_final: 0.8603 (tptm) REVERT: E 189 LYS cc_start: 0.7469 (mttt) cc_final: 0.6720 (tttm) REVERT: E 211 GLU cc_start: 0.8081 (tt0) cc_final: 0.7667 (tp30) REVERT: E 267 GLU cc_start: 0.6941 (mp0) cc_final: 0.6650 (mp0) REVERT: E 426 MET cc_start: 0.8338 (tpp) cc_final: 0.8136 (ttm) REVERT: E 479 TRP cc_start: 0.7771 (m-10) cc_final: 0.7353 (m-10) REVERT: E 504 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7545 (ttm110) REVERT: F 590 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8838 (mm110) REVERT: O 46 GLU cc_start: 0.8646 (tt0) cc_final: 0.8348 (tt0) REVERT: Q 53 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8368 (mm-40) REVERT: Q 87 TYR cc_start: 0.8462 (m-80) cc_final: 0.8103 (m-80) REVERT: P 71 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8556 (pmt-80) REVERT: P 76 ASP cc_start: 0.7155 (t70) cc_final: 0.6801 (m-30) REVERT: P 83 LYS cc_start: 0.7898 (mptt) cc_final: 0.7472 (mmtm) REVERT: P 105 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7596 (mmt180) outliers start: 24 outliers final: 7 residues processed: 495 average time/residue: 0.7640 time to fit residues: 426.1494 Evaluate side-chains 392 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 382 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 76 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain K residue 74 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 27 ASP Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain P residue 71 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN B 577 GLN C 114 GLN C 432 GLN D 653 GLN J 76 ASN M 69 ASN E 137 ASN F 577 GLN O 76 ASN Q 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.169856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.135365 restraints weight = 24208.418| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.00 r_work: 0.3192 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 25314 Z= 0.134 Angle : 0.586 8.624 34485 Z= 0.300 Chirality : 0.046 0.232 3954 Planarity : 0.004 0.064 4305 Dihedral : 8.249 67.908 4718 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.83 % Allowed : 12.07 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.15), residues: 2988 helix: 1.89 (0.27), residues: 402 sheet: 0.89 (0.16), residues: 1002 loop : 0.18 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 105 TYR 0.013 0.001 TYR G 91 PHE 0.017 0.002 PHE N 51 TRP 0.020 0.002 TRP C 479 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (25203) covalent geometry : angle 0.56556 / 0.30 (34194) SS BOND : bond 0.00377 / 0.22 ( 42) SS BOND : angle 1.20319 / 0.78 ( 84) hydrogen bonds : bond 0.04666 / 3.11 ( 654) hydrogen bonds : angle 5.22416 / 3.53 ( 1710) link_ALPHA1-3 : bond 0.01020 / 0.51 ( 3) link_ALPHA1-3 : angle 1.53170 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00096 / 0.05 ( 3) link_ALPHA1-6 : angle 2.32430 / 1.58 ( 9) link_BETA1-4 : bond 0.00363 / 0.23 ( 18) link_BETA1-4 : angle 2.01929 / 1.34 ( 54) link_NAG-ASN : bond 0.00337 / 0.20 ( 45) link_NAG-ASN : angle 1.88491 / 1.32 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.8548 (tp30) cc_final: 0.8106 (tp30) REVERT: A 121 LYS cc_start: 0.8996 (mttt) cc_final: 0.8490 (mmtt) REVERT: A 137 ASN cc_start: 0.6526 (m-40) cc_final: 0.6092 (m-40) REVERT: A 153 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7194 (mt-10) REVERT: A 189 LYS cc_start: 0.7311 (mttt) cc_final: 0.6465 (tttm) REVERT: A 211 GLU cc_start: 0.8149 (tt0) cc_final: 0.7783 (tp30) REVERT: A 315 GLN cc_start: 0.7823 (mt0) cc_final: 0.7585 (mm110) REVERT: A 335 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7904 (tttm) REVERT: A 479 TRP cc_start: 0.7926 (m-10) cc_final: 0.7456 (m-10) REVERT: A 504 ARG cc_start: 0.8264 (ttp80) cc_final: 0.7643 (tpm170) REVERT: I 86 TYR cc_start: 0.8145 (m-80) cc_final: 0.7928 (m-80) REVERT: I 87 TYR cc_start: 0.8494 (m-80) cc_final: 0.8019 (m-80) REVERT: H 51 MET cc_start: 0.9157 (tmm) cc_final: 0.8956 (tmm) REVERT: H 74 SER cc_start: 0.8625 (t) cc_final: 0.8276 (t) REVERT: H 75 GLN cc_start: 0.7956 (mt0) cc_final: 0.7456 (mp10) REVERT: H 100 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7840 (mmmt) REVERT: H 105 ARG cc_start: 0.8066 (mmt180) cc_final: 0.7221 (mmm-85) REVERT: C 95 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8994 (ptm) REVERT: C 121 LYS cc_start: 0.8863 (mttt) cc_final: 0.8459 (mmtt) REVERT: C 137 ASN cc_start: 0.6374 (m-40) cc_final: 0.5911 (m-40) REVERT: C 178 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7943 (tpt-90) REVERT: C 189 LYS cc_start: 0.7490 (mttt) cc_final: 0.6659 (tttm) REVERT: C 211 GLU cc_start: 0.8139 (tt0) cc_final: 0.7737 (tp30) REVERT: C 308 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7655 (mmm-85) REVERT: C 335 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7950 (ttpp) REVERT: J 34 MET cc_start: 0.8860 (mmm) cc_final: 0.8634 (mmt) REVERT: J 46 GLU cc_start: 0.8830 (tt0) cc_final: 0.8386 (tt0) REVERT: J 91 TYR cc_start: 0.8530 (m-80) cc_final: 0.8138 (m-80) REVERT: M 50 ASP cc_start: 0.8155 (m-30) cc_final: 0.7846 (m-30) REVERT: K 48 MET cc_start: 0.9226 (mtp) cc_final: 0.8971 (mtm) REVERT: K 69 MET cc_start: 0.9080 (mtt) cc_final: 0.8849 (mtt) REVERT: K 74 SER cc_start: 0.8709 (t) cc_final: 0.8371 (t) REVERT: K 75 GLN cc_start: 0.8018 (mt0) cc_final: 0.7437 (mp-120) REVERT: K 100 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8052 (mmmt) REVERT: K 105 ARG cc_start: 0.8204 (mmt180) cc_final: 0.7425 (mmm-85) REVERT: E 121 LYS cc_start: 0.8984 (mttt) cc_final: 0.8588 (mmtt) REVERT: E 189 LYS cc_start: 0.7413 (mttt) cc_final: 0.6556 (tttm) REVERT: E 211 GLU cc_start: 0.8059 (tt0) cc_final: 0.7641 (tp30) REVERT: E 267 GLU cc_start: 0.6983 (mp0) cc_final: 0.6706 (mp0) REVERT: E 302 ASN cc_start: 0.8096 (m-40) cc_final: 0.7752 (m-40) REVERT: E 305 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8171 (mtmm) REVERT: E 504 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7524 (ttm110) REVERT: F 632 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8217 (t70) REVERT: O 46 GLU cc_start: 0.8794 (tt0) cc_final: 0.8435 (tt0) REVERT: Q 53 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8468 (mm-40) REVERT: Q 87 TYR cc_start: 0.8437 (m-80) cc_final: 0.8173 (m-80) REVERT: P 72 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8183 (tt0) REVERT: P 74 SER cc_start: 0.8626 (t) cc_final: 0.8301 (t) REVERT: P 76 ASP cc_start: 0.7021 (t70) cc_final: 0.6786 (m-30) REVERT: P 105 ARG cc_start: 0.8078 (mmt180) cc_final: 0.7249 (mmm-85) outliers start: 48 outliers final: 22 residues processed: 435 average time/residue: 0.7828 time to fit residues: 382.4051 Evaluate side-chains 400 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 373 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain P residue 72 GLN Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 167 optimal weight: 0.0770 chunk 71 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 0.0970 chunk 146 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 267 optimal weight: 0.4980 overall best weight: 1.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 478 ASN B 577 GLN G 39 GLN I 38 GLN C 114 GLN C 478 ASN D 653 GLN J 76 ASN E 67 ASN E 422 GLN E 478 ASN F 577 GLN F 585 HIS O 39 GLN Q 31 ASN Q 38 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.164069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.129055 restraints weight = 24161.757| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.11 r_work: 0.3097 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 25314 Z= 0.243 Angle : 0.644 9.034 34485 Z= 0.330 Chirality : 0.048 0.220 3954 Planarity : 0.005 0.066 4305 Dihedral : 6.890 56.737 4704 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.86 % Allowed : 11.95 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.15), residues: 2988 helix: 1.22 (0.26), residues: 426 sheet: 0.82 (0.16), residues: 936 loop : 0.06 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 28 TYR 0.017 0.002 TYR H 32 PHE 0.017 0.002 PHE E 353 TRP 0.020 0.002 TRP C 479 HIS 0.004 0.001 HIS M 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (25203) covalent geometry : angle 0.62268 / 0.32 (34194) SS BOND : bond 0.00449 / 0.29 ( 42) SS BOND : angle 1.55147 / 1.02 ( 84) hydrogen bonds : bond 0.05218 / 3.43 ( 654) hydrogen bonds : angle 5.11173 / 3.44 ( 1710) link_ALPHA1-3 : bond 0.00846 / 0.42 ( 3) link_ALPHA1-3 : angle 1.36390 / 0.95 ( 9) link_ALPHA1-6 : bond 0.00070 / 0.04 ( 3) link_ALPHA1-6 : angle 2.29776 / 1.51 ( 9) link_BETA1-4 : bond 0.00345 / 0.21 ( 18) link_BETA1-4 : angle 2.00813 / 1.35 ( 54) link_NAG-ASN : bond 0.00431 / 0.26 ( 45) link_NAG-ASN : angle 2.01752 / 1.38 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 386 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9057 (mttt) cc_final: 0.8647 (mmtp) REVERT: A 137 ASN cc_start: 0.6391 (m-40) cc_final: 0.6121 (m-40) REVERT: A 153 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7266 (mt-10) REVERT: A 183 GLN cc_start: 0.8391 (tt0) cc_final: 0.8075 (tt0) REVERT: A 189 LYS cc_start: 0.7389 (mttt) cc_final: 0.6531 (tttm) REVERT: A 211 GLU cc_start: 0.8254 (tt0) cc_final: 0.7762 (tp30) REVERT: A 504 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7721 (tpm170) REVERT: I 86 TYR cc_start: 0.8370 (m-80) cc_final: 0.8021 (m-80) REVERT: I 87 TYR cc_start: 0.8811 (m-80) cc_final: 0.8503 (m-80) REVERT: I 94 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7504 (mtp85) REVERT: H 38 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7360 (ttm170) REVERT: H 74 SER cc_start: 0.8590 (t) cc_final: 0.8219 (t) REVERT: H 75 GLN cc_start: 0.7875 (mt0) cc_final: 0.7434 (mp10) REVERT: H 76 ASP cc_start: 0.8134 (t0) cc_final: 0.7886 (t0) REVERT: H 100 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7990 (mmmt) REVERT: H 105 ARG cc_start: 0.8092 (mmt180) cc_final: 0.7342 (mmm-85) REVERT: L 37 GLN cc_start: 0.7230 (tt0) cc_final: 0.6785 (tp40) REVERT: C 95 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8954 (ptm) REVERT: C 121 LYS cc_start: 0.8894 (mttt) cc_final: 0.8569 (mmtt) REVERT: C 137 ASN cc_start: 0.6472 (m-40) cc_final: 0.6018 (m-40) REVERT: C 178 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8093 (tpt-90) REVERT: C 189 LYS cc_start: 0.7573 (mttt) cc_final: 0.6683 (tttm) REVERT: C 211 GLU cc_start: 0.8265 (tt0) cc_final: 0.7823 (tp30) REVERT: C 308 ARG cc_start: 0.8007 (mmt-90) cc_final: 0.7643 (mmm-85) REVERT: C 335 LYS cc_start: 0.8389 (ttmt) cc_final: 0.7989 (ttpp) REVERT: J 34 MET cc_start: 0.8973 (mmm) cc_final: 0.8760 (mmt) REVERT: J 46 GLU cc_start: 0.8973 (tt0) cc_final: 0.8623 (tt0) REVERT: K 38 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7575 (ttm170) REVERT: K 48 MET cc_start: 0.9279 (mtp) cc_final: 0.9052 (mtm) REVERT: K 74 SER cc_start: 0.8770 (t) cc_final: 0.8432 (t) REVERT: K 75 GLN cc_start: 0.7930 (mt0) cc_final: 0.7366 (mp-120) REVERT: K 76 ASP cc_start: 0.7590 (t70) cc_final: 0.7050 (m-30) REVERT: K 76 ASP cc_start: 0.8242 (t0) cc_final: 0.7962 (t0) REVERT: K 105 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7480 (mmm-85) REVERT: E 121 LYS cc_start: 0.9070 (mttt) cc_final: 0.8711 (mmtt) REVERT: E 125 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8871 (mt) REVERT: E 137 ASN cc_start: 0.6375 (m-40) cc_final: 0.6023 (m-40) REVERT: E 178 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8158 (tpt-90) REVERT: E 189 LYS cc_start: 0.7551 (mttt) cc_final: 0.6664 (tttm) REVERT: E 211 GLU cc_start: 0.8216 (tt0) cc_final: 0.7781 (tp30) REVERT: E 305 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8224 (mtmm) REVERT: E 504 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7540 (tpm170) REVERT: F 632 ASP cc_start: 0.8545 (t70) cc_final: 0.8266 (t70) REVERT: O 46 GLU cc_start: 0.8887 (tt0) cc_final: 0.8518 (tt0) REVERT: Q 87 TYR cc_start: 0.8705 (m-80) cc_final: 0.8460 (m-80) REVERT: P 76 ASP cc_start: 0.7143 (t70) cc_final: 0.6835 (m-30) REVERT: P 105 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7315 (mmm-85) outliers start: 75 outliers final: 40 residues processed: 435 average time/residue: 0.7646 time to fit residues: 373.9284 Evaluate side-chains 418 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 613 SER Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 148 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 263 optimal weight: 0.3980 chunk 143 optimal weight: 0.9980 chunk 195 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 577 GLN C 114 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN E 315 GLN F 577 GLN O 100BGLN Q 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129677 restraints weight = 24160.474| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.08 r_work: 0.3114 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25314 Z= 0.180 Angle : 0.587 10.548 34485 Z= 0.302 Chirality : 0.046 0.211 3954 Planarity : 0.004 0.052 4305 Dihedral : 6.138 46.666 4702 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.86 % Allowed : 12.56 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.57 (0.15), residues: 2988 helix: 1.50 (0.26), residues: 408 sheet: 0.66 (0.16), residues: 954 loop : -0.01 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 28 TYR 0.018 0.002 TYR G 91 PHE 0.014 0.002 PHE E 53 TRP 0.017 0.002 TRP C 479 HIS 0.003 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (25203) covalent geometry : angle 0.56376 / 0.30 (34194) SS BOND : bond 0.00374 / 0.24 ( 42) SS BOND : angle 1.96020 / 1.29 ( 84) hydrogen bonds : bond 0.04587 / 3.02 ( 654) hydrogen bonds : angle 5.01549 / 3.37 ( 1710) link_ALPHA1-3 : bond 0.01158 / 0.58 ( 3) link_ALPHA1-3 : angle 1.13813 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00084 / 0.04 ( 3) link_ALPHA1-6 : angle 2.09599 / 1.33 ( 9) link_BETA1-4 : bond 0.00368 / 0.22 ( 18) link_BETA1-4 : angle 1.72558 / 1.17 ( 54) link_NAG-ASN : bond 0.00297 / 0.19 ( 45) link_NAG-ASN : angle 1.91409 / 1.31 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 379 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9032 (mttt) cc_final: 0.8601 (mmtt) REVERT: A 153 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7111 (mt-10) REVERT: A 183 GLN cc_start: 0.8424 (tt0) cc_final: 0.8114 (tt0) REVERT: A 189 LYS cc_start: 0.7377 (mttt) cc_final: 0.6558 (tttm) REVERT: A 211 GLU cc_start: 0.8245 (tt0) cc_final: 0.7759 (tp30) REVERT: A 308 ARG cc_start: 0.7961 (mmt-90) cc_final: 0.7744 (mmm160) REVERT: A 479 TRP cc_start: 0.8021 (m-10) cc_final: 0.6814 (m-10) REVERT: A 504 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7718 (tpm170) REVERT: G 34 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (mmt) REVERT: I 86 TYR cc_start: 0.8386 (m-80) cc_final: 0.8055 (m-80) REVERT: I 87 TYR cc_start: 0.8802 (m-80) cc_final: 0.8500 (m-80) REVERT: H 38 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7337 (ttm170) REVERT: H 74 SER cc_start: 0.8557 (t) cc_final: 0.8203 (t) REVERT: H 75 GLN cc_start: 0.7777 (mt0) cc_final: 0.7387 (mp-120) REVERT: H 76 ASP cc_start: 0.8090 (t0) cc_final: 0.7832 (t0) REVERT: H 100 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8045 (mmmt) REVERT: H 105 ARG cc_start: 0.8070 (mmt180) cc_final: 0.7269 (mmm-85) REVERT: C 95 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8983 (ptm) REVERT: C 121 LYS cc_start: 0.8946 (mttt) cc_final: 0.8635 (mmtt) REVERT: C 137 ASN cc_start: 0.6308 (m-40) cc_final: 0.5892 (m-40) REVERT: C 178 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8009 (tpt-90) REVERT: C 189 LYS cc_start: 0.7539 (mttt) cc_final: 0.6693 (tttm) REVERT: C 192 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8139 (ptm-80) REVERT: C 211 GLU cc_start: 0.8285 (tt0) cc_final: 0.7840 (tp30) REVERT: C 308 ARG cc_start: 0.7993 (mmt-90) cc_final: 0.7659 (mmm-85) REVERT: C 335 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8078 (ttpp) REVERT: J 23 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7567 (ttt180) REVERT: J 46 GLU cc_start: 0.8976 (tt0) cc_final: 0.8585 (tt0) REVERT: K 38 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: K 48 MET cc_start: 0.9281 (mtp) cc_final: 0.9053 (mtm) REVERT: K 75 GLN cc_start: 0.7860 (mt0) cc_final: 0.7351 (mp-120) REVERT: K 76 ASP cc_start: 0.7561 (t70) cc_final: 0.7060 (m-30) REVERT: E 49 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8697 (mt-10) REVERT: E 121 LYS cc_start: 0.9050 (mttt) cc_final: 0.8716 (mmtt) REVERT: E 137 ASN cc_start: 0.6433 (m-40) cc_final: 0.6084 (m-40) REVERT: E 189 LYS cc_start: 0.7507 (mttt) cc_final: 0.6602 (tttm) REVERT: E 211 GLU cc_start: 0.8267 (tt0) cc_final: 0.7818 (tp30) REVERT: E 305 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: E 504 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7533 (tpm170) REVERT: F 632 ASP cc_start: 0.8480 (t70) cc_final: 0.8206 (t70) REVERT: O 46 GLU cc_start: 0.8895 (tt0) cc_final: 0.8590 (tt0) REVERT: Q 87 TYR cc_start: 0.8764 (m-80) cc_final: 0.8543 (m-80) REVERT: P 51 MET cc_start: 0.9246 (tmm) cc_final: 0.8929 (tmm) REVERT: P 74 SER cc_start: 0.8590 (t) cc_final: 0.8268 (t) REVERT: P 76 ASP cc_start: 0.7121 (t70) cc_final: 0.6863 (m-30) REVERT: P 105 ARG cc_start: 0.8122 (mmt180) cc_final: 0.7364 (mmm-85) outliers start: 75 outliers final: 45 residues processed: 431 average time/residue: 0.7573 time to fit residues: 368.0710 Evaluate side-chains 417 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 364 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 56 SER Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 192 ARG Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 174 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 225 optimal weight: 0.4980 chunk 210 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 577 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN E 315 GLN Q 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.165370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131088 restraints weight = 24113.362| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25314 Z= 0.145 Angle : 0.547 10.010 34485 Z= 0.280 Chirality : 0.044 0.209 3954 Planarity : 0.004 0.043 4305 Dihedral : 5.533 37.128 4702 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.75 % Allowed : 12.98 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.62 (0.15), residues: 2988 helix: 1.41 (0.26), residues: 426 sheet: 0.65 (0.16), residues: 954 loop : 0.08 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 28 TYR 0.017 0.001 TYR G 91 PHE 0.012 0.001 PHE E 53 TRP 0.015 0.001 TRP P 50 HIS 0.002 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (25203) covalent geometry : angle 0.52414 / 0.27 (34194) SS BOND : bond 0.00392 / 0.22 ( 42) SS BOND : angle 1.86018 / 1.24 ( 84) hydrogen bonds : bond 0.04176 / 2.75 ( 654) hydrogen bonds : angle 4.84165 / 3.25 ( 1710) link_ALPHA1-3 : bond 0.01304 / 0.65 ( 3) link_ALPHA1-3 : angle 1.04051 / 0.76 ( 9) link_ALPHA1-6 : bond 0.00258 / 0.13 ( 3) link_ALPHA1-6 : angle 1.84009 / 1.16 ( 9) link_BETA1-4 : bond 0.00368 / 0.22 ( 18) link_BETA1-4 : angle 1.60216 / 1.09 ( 54) link_NAG-ASN : bond 0.00255 / 0.16 ( 45) link_NAG-ASN : angle 1.81491 / 1.24 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 371 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9039 (mttt) cc_final: 0.8615 (mmtt) REVERT: A 153 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7407 (mt-10) REVERT: A 183 GLN cc_start: 0.8437 (tt0) cc_final: 0.8125 (tt0) REVERT: A 211 GLU cc_start: 0.8277 (tt0) cc_final: 0.7726 (tp30) REVERT: A 308 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7684 (mmm160) REVERT: A 479 TRP cc_start: 0.8007 (m-10) cc_final: 0.6754 (m-10) REVERT: A 504 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7722 (tpm170) REVERT: I 86 TYR cc_start: 0.8407 (m-80) cc_final: 0.8068 (m-80) REVERT: I 87 TYR cc_start: 0.8791 (m-80) cc_final: 0.8486 (m-80) REVERT: I 94 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7504 (mtp85) REVERT: H 38 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7316 (ttm170) REVERT: H 74 SER cc_start: 0.8384 (t) cc_final: 0.8002 (t) REVERT: H 75 GLN cc_start: 0.7772 (mt0) cc_final: 0.7401 (mp-120) REVERT: H 85 ASP cc_start: 0.8294 (p0) cc_final: 0.7975 (p0) REVERT: H 100 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8045 (mmmt) REVERT: H 105 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7238 (mmm-85) REVERT: L 37 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6661 (tp40) REVERT: L 65 SER cc_start: 0.8136 (p) cc_final: 0.7753 (t) REVERT: C 92 GLU cc_start: 0.8717 (tp30) cc_final: 0.8513 (tp30) REVERT: C 95 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8975 (ptm) REVERT: C 121 LYS cc_start: 0.8958 (mttt) cc_final: 0.8601 (mmtt) REVERT: C 125 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8739 (mm) REVERT: C 137 ASN cc_start: 0.6076 (m-40) cc_final: 0.5684 (m-40) REVERT: C 178 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7963 (tpt-90) REVERT: C 189 LYS cc_start: 0.7538 (mttt) cc_final: 0.6689 (tttm) REVERT: C 211 GLU cc_start: 0.8296 (tt0) cc_final: 0.7815 (tp30) REVERT: C 308 ARG cc_start: 0.8003 (mmt-90) cc_final: 0.7687 (mmm-85) REVERT: C 335 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8067 (ttpp) REVERT: C 504 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7691 (ttp80) REVERT: J 23 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7613 (ttt180) REVERT: J 46 GLU cc_start: 0.8979 (tt0) cc_final: 0.8634 (tt0) REVERT: J 91 TYR cc_start: 0.8727 (m-80) cc_final: 0.8469 (m-80) REVERT: K 38 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7487 (ttm170) REVERT: K 48 MET cc_start: 0.9271 (mtp) cc_final: 0.9044 (mtm) REVERT: K 69 MET cc_start: 0.9224 (mtt) cc_final: 0.8919 (mtt) REVERT: K 75 GLN cc_start: 0.7872 (mt0) cc_final: 0.7378 (mp-120) REVERT: K 76 ASP cc_start: 0.7572 (t70) cc_final: 0.7049 (m-30) REVERT: E 121 LYS cc_start: 0.9086 (mttt) cc_final: 0.8746 (mmtt) REVERT: E 125 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8818 (mt) REVERT: E 137 ASN cc_start: 0.6240 (m-40) cc_final: 0.5964 (m-40) REVERT: E 178 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8091 (tpt-90) REVERT: E 189 LYS cc_start: 0.7488 (mttt) cc_final: 0.6577 (tttm) REVERT: E 211 GLU cc_start: 0.8234 (tt0) cc_final: 0.7754 (tp30) REVERT: E 305 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8242 (mtmm) REVERT: E 504 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7523 (tpm170) REVERT: F 632 ASP cc_start: 0.8502 (t70) cc_final: 0.8231 (t70) REVERT: O 46 GLU cc_start: 0.8906 (tt0) cc_final: 0.8636 (tt0) REVERT: Q 87 TYR cc_start: 0.8782 (m-80) cc_final: 0.8505 (m-80) REVERT: P 51 MET cc_start: 0.9238 (tmm) cc_final: 0.8930 (tmm) REVERT: P 74 SER cc_start: 0.8595 (t) cc_final: 0.8262 (t) REVERT: P 76 ASP cc_start: 0.7247 (t70) cc_final: 0.6887 (m-30) REVERT: P 76 ASP cc_start: 0.8019 (t0) cc_final: 0.7775 (t0) REVERT: P 105 ARG cc_start: 0.8112 (mmt180) cc_final: 0.7343 (mmm-85) outliers start: 72 outliers final: 40 residues processed: 428 average time/residue: 0.7470 time to fit residues: 360.4935 Evaluate side-chains 405 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 353 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 23 ARG Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain R residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 56 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 201 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 315 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN M 69 ASN O 76 ASN Q 31 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129087 restraints weight = 24158.912| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.04 r_work: 0.3090 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25314 Z= 0.191 Angle : 0.581 10.034 34485 Z= 0.297 Chirality : 0.046 0.212 3954 Planarity : 0.004 0.059 4305 Dihedral : 5.453 33.058 4702 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.36 % Allowed : 13.06 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.50 (0.15), residues: 2988 helix: 1.28 (0.26), residues: 426 sheet: 0.47 (0.16), residues: 939 loop : 0.10 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.019 0.002 TYR G 91 PHE 0.013 0.002 PHE E 353 TRP 0.015 0.002 TRP K 50 HIS 0.003 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (25203) covalent geometry : angle 0.55979 / 0.29 (34194) SS BOND : bond 0.00452 / 0.29 ( 42) SS BOND : angle 1.74567 / 1.18 ( 84) hydrogen bonds : bond 0.04583 / 3.01 ( 654) hydrogen bonds : angle 4.90837 / 3.29 ( 1710) link_ALPHA1-3 : bond 0.01230 / 0.62 ( 3) link_ALPHA1-3 : angle 1.11031 / 0.83 ( 9) link_ALPHA1-6 : bond 0.00290 / 0.14 ( 3) link_ALPHA1-6 : angle 1.79932 / 1.12 ( 9) link_BETA1-4 : bond 0.00346 / 0.21 ( 18) link_BETA1-4 : angle 1.67864 / 1.14 ( 54) link_NAG-ASN : bond 0.00343 / 0.22 ( 45) link_NAG-ASN : angle 1.90876 / 1.29 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 361 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.9108 (mttt) cc_final: 0.8691 (mmtt) REVERT: A 183 GLN cc_start: 0.8451 (tt0) cc_final: 0.8152 (tt0) REVERT: A 211 GLU cc_start: 0.8292 (tt0) cc_final: 0.7715 (tp30) REVERT: A 308 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7694 (mmm160) REVERT: A 504 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7741 (tpm170) REVERT: I 86 TYR cc_start: 0.8411 (m-80) cc_final: 0.8075 (m-80) REVERT: I 94 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7644 (mtp85) REVERT: H 38 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: H 74 SER cc_start: 0.8519 (t) cc_final: 0.8179 (t) REVERT: H 75 GLN cc_start: 0.7759 (mt0) cc_final: 0.7326 (mp-120) REVERT: H 76 ASP cc_start: 0.8029 (t0) cc_final: 0.7773 (t0) REVERT: H 85 ASP cc_start: 0.8334 (p0) cc_final: 0.8015 (p0) REVERT: H 105 ARG cc_start: 0.8089 (mmt180) cc_final: 0.7207 (mmm-85) REVERT: L 37 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6783 (tp40) REVERT: L 65 SER cc_start: 0.8108 (p) cc_final: 0.7746 (t) REVERT: C 95 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8978 (ptm) REVERT: C 121 LYS cc_start: 0.8982 (mttt) cc_final: 0.8608 (mmtt) REVERT: C 137 ASN cc_start: 0.6065 (m-40) cc_final: 0.5679 (m-40) REVERT: C 178 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7889 (tpt-90) REVERT: C 189 LYS cc_start: 0.7598 (mttt) cc_final: 0.6730 (tttm) REVERT: C 211 GLU cc_start: 0.8303 (tt0) cc_final: 0.7833 (tp30) REVERT: C 308 ARG cc_start: 0.7982 (mmt-90) cc_final: 0.7671 (mmm-85) REVERT: C 335 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8074 (ttpp) REVERT: C 419 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7740 (mtp85) REVERT: C 504 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7679 (ttp80) REVERT: J 46 GLU cc_start: 0.8984 (tt0) cc_final: 0.8651 (tt0) REVERT: K 38 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7613 (ttm170) REVERT: K 48 MET cc_start: 0.9289 (mtp) cc_final: 0.9058 (mtm) REVERT: K 75 GLN cc_start: 0.7878 (mt0) cc_final: 0.7380 (mp-120) REVERT: K 76 ASP cc_start: 0.7689 (t70) cc_final: 0.7129 (m-30) REVERT: E 121 LYS cc_start: 0.9119 (mttt) cc_final: 0.8759 (mmtt) REVERT: E 137 ASN cc_start: 0.6294 (m-40) cc_final: 0.5981 (m-40) REVERT: E 178 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8005 (tpt-90) REVERT: E 189 LYS cc_start: 0.7505 (mttt) cc_final: 0.6612 (tttm) REVERT: E 211 GLU cc_start: 0.8293 (tt0) cc_final: 0.7824 (tp30) REVERT: E 305 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8248 (mtmm) REVERT: E 504 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7542 (tpm170) REVERT: F 535 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: F 632 ASP cc_start: 0.8501 (t70) cc_final: 0.8228 (t70) REVERT: O 46 GLU cc_start: 0.8908 (tt0) cc_final: 0.8644 (tt0) REVERT: Q 87 TYR cc_start: 0.8791 (m-80) cc_final: 0.8519 (m-80) REVERT: P 51 MET cc_start: 0.9257 (tmm) cc_final: 0.8943 (tmm) REVERT: P 69 MET cc_start: 0.9048 (mtt) cc_final: 0.8680 (mtt) REVERT: P 74 SER cc_start: 0.8538 (t) cc_final: 0.8202 (t) REVERT: P 76 ASP cc_start: 0.7301 (t70) cc_final: 0.6934 (m-30) REVERT: P 76 ASP cc_start: 0.8039 (t0) cc_final: 0.7803 (t0) REVERT: P 105 ARG cc_start: 0.8122 (mmt180) cc_final: 0.7352 (mmm-85) REVERT: R 65 SER cc_start: 0.8089 (p) cc_final: 0.7748 (t) outliers start: 88 outliers final: 52 residues processed: 425 average time/residue: 0.7379 time to fit residues: 353.7159 Evaluate side-chains 419 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 356 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 65 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN B 577 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN O 76 ASN Q 31 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.164545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.129112 restraints weight = 24122.779| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.13 r_work: 0.3108 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25314 Z= 0.168 Angle : 0.557 8.766 34485 Z= 0.286 Chirality : 0.045 0.213 3954 Planarity : 0.004 0.051 4305 Dihedral : 5.281 31.248 4702 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.83 % Allowed : 14.09 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.52 (0.15), residues: 2988 helix: 1.30 (0.26), residues: 426 sheet: 0.46 (0.16), residues: 939 loop : 0.13 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.019 0.002 TYR G 91 PHE 0.011 0.002 PHE E 53 TRP 0.016 0.002 TRP H 50 HIS 0.003 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (25203) covalent geometry : angle 0.53612 / 0.28 (34194) SS BOND : bond 0.00381 / 0.23 ( 42) SS BOND : angle 1.69481 / 1.22 ( 84) hydrogen bonds : bond 0.04364 / 2.88 ( 654) hydrogen bonds : angle 4.86442 / 3.27 ( 1710) link_ALPHA1-3 : bond 0.01339 / 0.67 ( 3) link_ALPHA1-3 : angle 1.05660 / 0.80 ( 9) link_ALPHA1-6 : bond 0.00338 / 0.17 ( 3) link_ALPHA1-6 : angle 1.71084 / 1.06 ( 9) link_BETA1-4 : bond 0.00359 / 0.22 ( 18) link_BETA1-4 : angle 1.60294 / 1.09 ( 54) link_NAG-ASN : bond 0.00267 / 0.17 ( 45) link_NAG-ASN : angle 1.85977 / 1.26 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 365 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8213 (mt0) cc_final: 0.7952 (mm-40) REVERT: A 121 LYS cc_start: 0.9084 (mttt) cc_final: 0.8671 (mmtt) REVERT: A 183 GLN cc_start: 0.8453 (tt0) cc_final: 0.8158 (tt0) REVERT: A 211 GLU cc_start: 0.8266 (tt0) cc_final: 0.7675 (tp30) REVERT: A 308 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7702 (mmm160) REVERT: A 504 ARG cc_start: 0.8275 (ttp80) cc_final: 0.7724 (tpm170) REVERT: G 34 MET cc_start: 0.8697 (mmt) cc_final: 0.8494 (mmt) REVERT: I 86 TYR cc_start: 0.8424 (m-80) cc_final: 0.8079 (m-80) REVERT: I 94 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7568 (mtp85) REVERT: H 38 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7334 (ttm170) REVERT: H 74 SER cc_start: 0.8364 (t) cc_final: 0.7989 (t) REVERT: H 75 GLN cc_start: 0.7791 (mt0) cc_final: 0.7296 (mp-120) REVERT: H 76 ASP cc_start: 0.7961 (t0) cc_final: 0.7691 (t0) REVERT: H 85 ASP cc_start: 0.8333 (p0) cc_final: 0.8008 (p0) REVERT: H 105 ARG cc_start: 0.8099 (mmt180) cc_final: 0.7209 (mmm-85) REVERT: L 65 SER cc_start: 0.8095 (p) cc_final: 0.7742 (t) REVERT: C 95 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8969 (ptm) REVERT: C 121 LYS cc_start: 0.8960 (mttt) cc_final: 0.8570 (mmtt) REVERT: C 137 ASN cc_start: 0.6048 (m-40) cc_final: 0.5685 (m-40) REVERT: C 178 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7931 (tpt-90) REVERT: C 189 LYS cc_start: 0.7607 (mttt) cc_final: 0.6716 (tttm) REVERT: C 211 GLU cc_start: 0.8284 (tt0) cc_final: 0.7797 (tp30) REVERT: C 308 ARG cc_start: 0.8015 (mmt-90) cc_final: 0.7660 (mmm-85) REVERT: C 335 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8076 (ttpp) REVERT: C 419 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7740 (mtp85) REVERT: C 504 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7689 (ttp80) REVERT: D 653 GLN cc_start: 0.8908 (tt0) cc_final: 0.8701 (tt0) REVERT: J 46 GLU cc_start: 0.8967 (tt0) cc_final: 0.8625 (tt0) REVERT: K 38 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7502 (ttm170) REVERT: K 48 MET cc_start: 0.9270 (mtp) cc_final: 0.9027 (mtm) REVERT: K 69 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8914 (mtt) REVERT: K 75 GLN cc_start: 0.7884 (mt0) cc_final: 0.7366 (mp-120) REVERT: K 76 ASP cc_start: 0.7694 (t70) cc_final: 0.7111 (m-30) REVERT: N 65 SER cc_start: 0.7614 (p) cc_final: 0.7234 (t) REVERT: E 121 LYS cc_start: 0.9108 (mttt) cc_final: 0.8714 (mmtt) REVERT: E 137 ASN cc_start: 0.6239 (m-40) cc_final: 0.5935 (m-40) REVERT: E 178 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7992 (tpt-90) REVERT: E 189 LYS cc_start: 0.7497 (mttt) cc_final: 0.6567 (tttm) REVERT: E 211 GLU cc_start: 0.8269 (tt0) cc_final: 0.7791 (tp30) REVERT: E 305 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8230 (mtmm) REVERT: E 504 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7534 (tpm170) REVERT: F 632 ASP cc_start: 0.8495 (t70) cc_final: 0.8214 (t70) REVERT: F 633 LYS cc_start: 0.8535 (mttp) cc_final: 0.7839 (mtmt) REVERT: O 46 GLU cc_start: 0.8900 (tt0) cc_final: 0.8537 (tm-30) REVERT: Q 87 TYR cc_start: 0.8807 (m-80) cc_final: 0.8545 (m-80) REVERT: P 51 MET cc_start: 0.9243 (tmm) cc_final: 0.8933 (tmm) REVERT: P 74 SER cc_start: 0.8544 (t) cc_final: 0.8243 (t) REVERT: P 76 ASP cc_start: 0.7315 (t70) cc_final: 0.6919 (m-30) REVERT: P 105 ARG cc_start: 0.8123 (mmt180) cc_final: 0.7346 (mmm-85) REVERT: R 65 SER cc_start: 0.8068 (p) cc_final: 0.7763 (t) outliers start: 74 outliers final: 46 residues processed: 420 average time/residue: 0.7443 time to fit residues: 352.7747 Evaluate side-chains 411 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 355 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain O residue 110 THR Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 208 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.0980 chunk 59 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN J 76 ASN K 72 GLN O 76 ASN Q 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.164238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129093 restraints weight = 24102.914| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.19 r_work: 0.3099 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25314 Z= 0.174 Angle : 0.563 8.251 34485 Z= 0.288 Chirality : 0.045 0.215 3954 Planarity : 0.004 0.052 4305 Dihedral : 5.218 30.205 4701 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.86 % Allowed : 14.55 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.15), residues: 2988 helix: 1.25 (0.26), residues: 426 sheet: 0.43 (0.16), residues: 939 loop : 0.12 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.019 0.002 TYR G 91 PHE 0.011 0.002 PHE E 353 TRP 0.015 0.002 TRP P 50 HIS 0.003 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (25203) covalent geometry : angle 0.54148 / 0.28 (34194) SS BOND : bond 0.00403 / 0.26 ( 42) SS BOND : angle 1.65379 / 1.18 ( 84) hydrogen bonds : bond 0.04397 / 2.90 ( 654) hydrogen bonds : angle 4.87819 / 3.28 ( 1710) link_ALPHA1-3 : bond 0.01314 / 0.66 ( 3) link_ALPHA1-3 : angle 1.11638 / 0.85 ( 9) link_ALPHA1-6 : bond 0.00382 / 0.19 ( 3) link_ALPHA1-6 : angle 1.65835 / 1.03 ( 9) link_BETA1-4 : bond 0.00347 / 0.21 ( 18) link_BETA1-4 : angle 1.62041 / 1.10 ( 54) link_NAG-ASN : bond 0.00298 / 0.19 ( 45) link_NAG-ASN : angle 1.88535 / 1.28 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 362 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLN cc_start: 0.8208 (mt0) cc_final: 0.7927 (mm110) REVERT: A 121 LYS cc_start: 0.9084 (mttt) cc_final: 0.8661 (mmtt) REVERT: A 183 GLN cc_start: 0.8451 (tt0) cc_final: 0.8145 (tt0) REVERT: A 211 GLU cc_start: 0.8264 (tt0) cc_final: 0.7665 (tp30) REVERT: A 308 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7693 (mmm160) REVERT: A 504 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7724 (tpm170) REVERT: G 34 MET cc_start: 0.8749 (mmt) cc_final: 0.8541 (mmt) REVERT: I 86 TYR cc_start: 0.8407 (m-80) cc_final: 0.8000 (m-80) REVERT: I 94 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: H 38 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7301 (ttm170) REVERT: H 74 SER cc_start: 0.8490 (t) cc_final: 0.8113 (t) REVERT: H 76 ASP cc_start: 0.7886 (t0) cc_final: 0.7617 (t0) REVERT: H 85 ASP cc_start: 0.8302 (p0) cc_final: 0.7981 (p0) REVERT: H 100 LYS cc_start: 0.8471 (mmtt) cc_final: 0.8095 (mmmt) REVERT: H 105 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7156 (mmm-85) REVERT: L 65 SER cc_start: 0.7842 (p) cc_final: 0.7463 (t) REVERT: C 95 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8981 (ptm) REVERT: C 121 LYS cc_start: 0.8952 (mttt) cc_final: 0.8555 (mmtt) REVERT: C 137 ASN cc_start: 0.6049 (m-40) cc_final: 0.5659 (m-40) REVERT: C 178 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7889 (tpt-90) REVERT: C 189 LYS cc_start: 0.7589 (mttt) cc_final: 0.6705 (tttm) REVERT: C 211 GLU cc_start: 0.8249 (tt0) cc_final: 0.7764 (tp30) REVERT: C 308 ARG cc_start: 0.8005 (mmt-90) cc_final: 0.7613 (mmm-85) REVERT: C 315 GLN cc_start: 0.8150 (mt0) cc_final: 0.7943 (mt0) REVERT: C 335 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8070 (ttpp) REVERT: C 419 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7743 (mtp85) REVERT: C 504 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7672 (ttp80) REVERT: J 46 GLU cc_start: 0.8980 (tt0) cc_final: 0.8640 (tt0) REVERT: K 38 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7562 (ttm170) REVERT: K 48 MET cc_start: 0.9265 (mtp) cc_final: 0.9030 (mtm) REVERT: K 69 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8933 (mtt) REVERT: K 75 GLN cc_start: 0.7860 (mt0) cc_final: 0.7330 (mp-120) REVERT: K 76 ASP cc_start: 0.7677 (t70) cc_final: 0.7088 (m-30) REVERT: N 65 SER cc_start: 0.7590 (p) cc_final: 0.7222 (t) REVERT: E 121 LYS cc_start: 0.9102 (mttt) cc_final: 0.8705 (mmtt) REVERT: E 137 ASN cc_start: 0.6229 (m-40) cc_final: 0.5924 (m-40) REVERT: E 178 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8022 (tpt-90) REVERT: E 189 LYS cc_start: 0.7520 (mttt) cc_final: 0.6623 (tttm) REVERT: E 211 GLU cc_start: 0.8262 (tt0) cc_final: 0.7790 (tp30) REVERT: E 305 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8239 (mtmm) REVERT: E 504 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7538 (tpm170) REVERT: F 632 ASP cc_start: 0.8501 (t70) cc_final: 0.8218 (t70) REVERT: F 633 LYS cc_start: 0.8503 (mttp) cc_final: 0.7774 (mtmt) REVERT: O 23 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7454 (ttt90) REVERT: O 46 GLU cc_start: 0.8911 (tt0) cc_final: 0.8544 (tm-30) REVERT: Q 87 TYR cc_start: 0.8813 (m-80) cc_final: 0.8557 (m-80) REVERT: P 51 MET cc_start: 0.9259 (tmm) cc_final: 0.9006 (tmm) REVERT: P 74 SER cc_start: 0.8555 (t) cc_final: 0.8223 (t) REVERT: P 76 ASP cc_start: 0.7304 (t70) cc_final: 0.6907 (m-30) REVERT: P 105 ARG cc_start: 0.8152 (mmt180) cc_final: 0.7358 (mmm-85) REVERT: R 65 SER cc_start: 0.8059 (p) cc_final: 0.7744 (t) outliers start: 75 outliers final: 51 residues processed: 415 average time/residue: 0.7672 time to fit residues: 359.3886 Evaluate side-chains 418 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 356 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 192 ARG Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 110 optimal weight: 1.9990 chunk 288 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 200 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN O 76 ASN Q 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.165313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129965 restraints weight = 24181.598| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.14 r_work: 0.3115 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25314 Z= 0.141 Angle : 0.531 8.042 34485 Z= 0.272 Chirality : 0.044 0.214 3954 Planarity : 0.004 0.051 4305 Dihedral : 5.033 28.504 4701 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.52 % Allowed : 14.74 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.15), residues: 2988 helix: 1.41 (0.26), residues: 426 sheet: 0.45 (0.17), residues: 939 loop : 0.16 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.018 0.001 TYR G 91 PHE 0.010 0.001 PHE L 51 TRP 0.016 0.001 TRP P 50 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (25203) covalent geometry : angle 0.51196 / 0.27 (34194) SS BOND : bond 0.00344 / 0.21 ( 42) SS BOND : angle 1.45204 / 1.03 ( 84) hydrogen bonds : bond 0.04078 / 2.68 ( 654) hydrogen bonds : angle 4.77685 / 3.20 ( 1710) link_ALPHA1-3 : bond 0.01382 / 0.69 ( 3) link_ALPHA1-3 : angle 1.12646 / 0.86 ( 9) link_ALPHA1-6 : bond 0.00476 / 0.24 ( 3) link_ALPHA1-6 : angle 1.56721 / 0.98 ( 9) link_BETA1-4 : bond 0.00364 / 0.22 ( 18) link_BETA1-4 : angle 1.53283 / 1.04 ( 54) link_NAG-ASN : bond 0.00234 / 0.15 ( 45) link_NAG-ASN : angle 1.80582 / 1.22 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 354 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 CYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4587 (m) REVERT: A 82 GLN cc_start: 0.8209 (mt0) cc_final: 0.7938 (mm110) REVERT: A 103 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: A 121 LYS cc_start: 0.9077 (mttt) cc_final: 0.8654 (mmtt) REVERT: A 183 GLN cc_start: 0.8448 (tt0) cc_final: 0.8078 (tt0) REVERT: A 211 GLU cc_start: 0.8268 (tt0) cc_final: 0.7676 (tp30) REVERT: A 308 ARG cc_start: 0.7928 (mmt-90) cc_final: 0.7698 (mmm160) REVERT: A 504 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7729 (tpm170) REVERT: G 34 MET cc_start: 0.8732 (mmt) cc_final: 0.8511 (mmt) REVERT: I 86 TYR cc_start: 0.8396 (m-80) cc_final: 0.8060 (m-80) REVERT: I 94 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7479 (mtp85) REVERT: H 38 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7314 (ttm170) REVERT: H 85 ASP cc_start: 0.8293 (p0) cc_final: 0.7970 (p0) REVERT: H 100 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8098 (mmmt) REVERT: H 105 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7224 (mmm-85) REVERT: L 65 SER cc_start: 0.7882 (p) cc_final: 0.7508 (t) REVERT: C 95 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8991 (ptm) REVERT: C 121 LYS cc_start: 0.8960 (mttt) cc_final: 0.8560 (mmtt) REVERT: C 137 ASN cc_start: 0.6050 (m-40) cc_final: 0.5623 (m-40) REVERT: C 178 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7839 (tpt-90) REVERT: C 189 LYS cc_start: 0.7606 (mttt) cc_final: 0.6746 (tttm) REVERT: C 211 GLU cc_start: 0.8260 (tt0) cc_final: 0.7778 (tp30) REVERT: C 335 LYS cc_start: 0.8370 (ttmt) cc_final: 0.8037 (ttpp) REVERT: C 419 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7747 (mtp85) REVERT: C 504 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7688 (ttp80) REVERT: J 46 GLU cc_start: 0.8977 (tt0) cc_final: 0.8655 (tt0) REVERT: J 91 TYR cc_start: 0.8789 (m-80) cc_final: 0.8531 (m-80) REVERT: K 38 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7420 (ttm170) REVERT: K 48 MET cc_start: 0.9263 (mtp) cc_final: 0.9038 (mtm) REVERT: K 69 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8922 (mtt) REVERT: K 75 GLN cc_start: 0.7816 (mt0) cc_final: 0.7354 (mp-120) REVERT: K 76 ASP cc_start: 0.7645 (t70) cc_final: 0.7103 (m-30) REVERT: K 82 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7504 (mtm-85) REVERT: N 65 SER cc_start: 0.7608 (p) cc_final: 0.7245 (t) REVERT: E 121 LYS cc_start: 0.9094 (mttt) cc_final: 0.8710 (mmtt) REVERT: E 137 ASN cc_start: 0.6214 (m-40) cc_final: 0.5904 (m-40) REVERT: E 189 LYS cc_start: 0.7517 (mttt) cc_final: 0.6583 (tttm) REVERT: E 211 GLU cc_start: 0.8259 (tt0) cc_final: 0.7775 (tp30) REVERT: E 305 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8235 (mtmm) REVERT: E 308 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7973 (mmm160) REVERT: E 504 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7552 (tpm170) REVERT: F 632 ASP cc_start: 0.8489 (t70) cc_final: 0.8208 (t70) REVERT: F 633 LYS cc_start: 0.8477 (mttp) cc_final: 0.7778 (mtmt) REVERT: O 23 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7489 (ttt90) REVERT: O 46 GLU cc_start: 0.8906 (tt0) cc_final: 0.8557 (tm-30) REVERT: Q 87 TYR cc_start: 0.8802 (m-80) cc_final: 0.8553 (m-80) REVERT: P 74 SER cc_start: 0.8468 (t) cc_final: 0.8139 (t) REVERT: P 76 ASP cc_start: 0.7281 (t70) cc_final: 0.6902 (m-30) REVERT: P 105 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7357 (mmm-85) REVERT: R 65 SER cc_start: 0.8040 (p) cc_final: 0.7758 (t) outliers start: 66 outliers final: 46 residues processed: 404 average time/residue: 0.7544 time to fit residues: 343.1928 Evaluate side-chains 404 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 346 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 178 ARG Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 221 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 13 optimal weight: 0.0470 chunk 133 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 231 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 GLN C 114 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN K 72 GLN Q 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.165448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130854 restraints weight = 23994.862| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.93 r_work: 0.3131 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25314 Z= 0.138 Angle : 0.526 7.003 34485 Z= 0.270 Chirality : 0.044 0.213 3954 Planarity : 0.004 0.050 4305 Dihedral : 4.938 27.367 4701 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.52 % Allowed : 15.01 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.15), residues: 2988 helix: 1.40 (0.26), residues: 426 sheet: 0.45 (0.17), residues: 939 loop : 0.18 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.020 0.001 TYR G 91 PHE 0.010 0.001 PHE L 51 TRP 0.015 0.001 TRP H 50 HIS 0.002 0.001 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (25203) covalent geometry : angle 0.50647 / 0.27 (34194) SS BOND : bond 0.00338 / 0.21 ( 42) SS BOND : angle 1.38024 / 0.98 ( 84) hydrogen bonds : bond 0.04042 / 2.66 ( 654) hydrogen bonds : angle 4.76456 / 3.20 ( 1710) link_ALPHA1-3 : bond 0.01334 / 0.67 ( 3) link_ALPHA1-3 : angle 1.16813 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00513 / 0.26 ( 3) link_ALPHA1-6 : angle 1.53527 / 0.96 ( 9) link_BETA1-4 : bond 0.00353 / 0.22 ( 18) link_BETA1-4 : angle 1.53262 / 1.04 ( 54) link_NAG-ASN : bond 0.00237 / 0.15 ( 45) link_NAG-ASN : angle 1.79019 / 1.20 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5976 Ramachandran restraints generated. 2988 Oldfield, 0 Emsley, 2988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 352 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 74 CYS cc_start: 0.4925 (OUTLIER) cc_final: 0.4623 (m) REVERT: A 82 GLN cc_start: 0.8175 (mt0) cc_final: 0.7925 (mm110) REVERT: A 103 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7978 (tt0) REVERT: A 121 LYS cc_start: 0.9047 (mttt) cc_final: 0.8607 (mmtt) REVERT: A 183 GLN cc_start: 0.8399 (tt0) cc_final: 0.8064 (tt0) REVERT: A 211 GLU cc_start: 0.8210 (tt0) cc_final: 0.7616 (tp30) REVERT: A 308 ARG cc_start: 0.7893 (mmt-90) cc_final: 0.7641 (mmm160) REVERT: A 479 TRP cc_start: 0.7973 (m-10) cc_final: 0.6634 (m-10) REVERT: A 504 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7709 (tpm170) REVERT: G 34 MET cc_start: 0.8721 (mmt) cc_final: 0.8511 (mmt) REVERT: I 86 TYR cc_start: 0.8361 (m-80) cc_final: 0.8013 (m-80) REVERT: I 94 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7455 (mtp85) REVERT: H 38 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7221 (ttm170) REVERT: H 85 ASP cc_start: 0.8322 (p0) cc_final: 0.8014 (p0) REVERT: H 100 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8090 (mmmt) REVERT: H 105 ARG cc_start: 0.8046 (mmt180) cc_final: 0.7157 (mmm-85) REVERT: L 65 SER cc_start: 0.7812 (p) cc_final: 0.7453 (t) REVERT: C 95 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8966 (ptm) REVERT: C 121 LYS cc_start: 0.8925 (mttt) cc_final: 0.8508 (mmtt) REVERT: C 137 ASN cc_start: 0.6034 (m-40) cc_final: 0.5615 (m-40) REVERT: C 189 LYS cc_start: 0.7583 (mttt) cc_final: 0.6726 (tttm) REVERT: C 211 GLU cc_start: 0.8227 (tt0) cc_final: 0.7745 (tp30) REVERT: C 335 LYS cc_start: 0.8335 (ttmt) cc_final: 0.8001 (ttpp) REVERT: C 419 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7719 (mtp85) REVERT: C 504 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: J 46 GLU cc_start: 0.8949 (tt0) cc_final: 0.8616 (tt0) REVERT: J 91 TYR cc_start: 0.8745 (m-80) cc_final: 0.8463 (m-80) REVERT: M 94 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7538 (mtp180) REVERT: K 38 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7423 (ttm170) REVERT: K 48 MET cc_start: 0.9232 (mtp) cc_final: 0.9008 (mtm) REVERT: K 69 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8899 (mtt) REVERT: K 76 ASP cc_start: 0.7603 (t70) cc_final: 0.7085 (m-30) REVERT: K 82 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7451 (mtm-85) REVERT: N 65 SER cc_start: 0.7549 (p) cc_final: 0.7197 (t) REVERT: E 121 LYS cc_start: 0.9047 (mttt) cc_final: 0.8665 (mmtt) REVERT: E 125 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8380 (mt) REVERT: E 137 ASN cc_start: 0.6147 (m-40) cc_final: 0.5853 (m-40) REVERT: E 189 LYS cc_start: 0.7468 (mttt) cc_final: 0.6529 (tttm) REVERT: E 211 GLU cc_start: 0.8217 (tt0) cc_final: 0.7757 (tp30) REVERT: E 305 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8196 (mtmm) REVERT: E 504 ARG cc_start: 0.8122 (ttp80) cc_final: 0.7524 (tpm170) REVERT: F 632 ASP cc_start: 0.8465 (t70) cc_final: 0.8167 (t70) REVERT: F 633 LYS cc_start: 0.8446 (mttp) cc_final: 0.7725 (mtmt) REVERT: O 23 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7442 (ttt90) REVERT: O 46 GLU cc_start: 0.8872 (tt0) cc_final: 0.8512 (tm-30) REVERT: Q 87 TYR cc_start: 0.8781 (m-80) cc_final: 0.8462 (m-80) REVERT: P 74 SER cc_start: 0.8446 (t) cc_final: 0.8140 (t) REVERT: P 76 ASP cc_start: 0.7153 (t70) cc_final: 0.6862 (m-30) REVERT: P 105 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7308 (mmm-85) REVERT: R 65 SER cc_start: 0.7984 (p) cc_final: 0.7721 (t) outliers start: 66 outliers final: 48 residues processed: 403 average time/residue: 0.7488 time to fit residues: 340.8149 Evaluate side-chains 406 residues out of total 2619 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 103 GLN Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 601 LYS Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 647 GLU Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain I residue 94 ARG Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 504 ARG Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 305 LYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 505 VAL Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain O residue 23 ARG Chi-restraints excluded: chain O residue 60 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain Q residue 34 SER Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain R residue 11 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 36 optimal weight: 0.1980 chunk 281 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 162 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 234 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 260 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 207 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 315 GLN G 39 GLN I 38 GLN C 114 GLN C 315 GLN C 432 GLN D 577 GLN D 616 ASN D 653 GLN J 76 ASN Q 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.166224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.131415 restraints weight = 24096.788| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.00 r_work: 0.3133 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25314 Z= 0.124 Angle : 0.512 6.988 34485 Z= 0.263 Chirality : 0.043 0.213 3954 Planarity : 0.004 0.049 4305 Dihedral : 4.823 26.114 4701 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.33 % Allowed : 15.31 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.15), residues: 2988 helix: 1.50 (0.26), residues: 426 sheet: 0.46 (0.17), residues: 939 loop : 0.20 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 28 TYR 0.019 0.001 TYR G 91 PHE 0.010 0.001 PHE L 51 TRP 0.015 0.001 TRP H 50 HIS 0.002 0.000 HIS G 82A Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 (25203) covalent geometry : angle 0.49389 / 0.26 (34194) SS BOND : bond 0.00321 / 0.20 ( 42) SS BOND : angle 1.28065 / 0.91 ( 84) hydrogen bonds : bond 0.03873 / 2.54 ( 654) hydrogen bonds : angle 4.70705 / 3.16 ( 1710) link_ALPHA1-3 : bond 0.01355 / 0.68 ( 3) link_ALPHA1-3 : angle 1.18544 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00545 / 0.27 ( 3) link_ALPHA1-6 : angle 1.49450 / 0.94 ( 9) link_BETA1-4 : bond 0.00369 / 0.23 ( 18) link_BETA1-4 : angle 1.48862 / 1.01 ( 54) link_NAG-ASN : bond 0.00218 / 0.14 ( 45) link_NAG-ASN : angle 1.77260 / 1.19 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10595.50 seconds wall clock time: 180 minutes 35.25 seconds (10835.25 seconds total)