Starting phenix.real_space_refine on Sun Jul 5 03:11:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.map" model { file = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dow_27624/07_2026/8dow_27624.cif" } resolution = 3.69 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= 0.003 sd= 0.136 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 138 5.16 5 C 15658 2.51 5 N 4220 2.21 5 O 5037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25053 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "C" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "E" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "F" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "H" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "I" Number of atoms: 3613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3613 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 23, 'TRANS': 438} Chain: "J" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1725 Classifications: {'peptide': 225} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 212} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1676 Classifications: {'peptide': 217} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "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 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 chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "b" 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 chiralities: 3 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.33, per 1000 atoms: 0.21 Number of scatterers: 25053 At special positions: 0 Unit cell: (184.68, 195.48, 158.76, 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 138 16.00 O 5037 8.00 N 4220 7.00 C 15658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 152 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 155 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.04 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 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 139 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.04 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.03 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 155 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.05 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.02 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.03 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.04 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 152 " - pdb=" SG CYS K 208 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " 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 N 3 " - " MAN N 6 " " MAN N 4 " - " MAN N 5 " " BMA S 3 " - " MAN S 6 " " MAN S 4 " - " MAN S 5 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " ALPHA1-6 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA a 3 " - " MAN a 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " NAG-ASN " NAG A 601 " - " ASN A 154 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 355 " " NAG A 605 " - " ASN A 448 " " NAG A 606 " - " ASN A 234 " " NAG E 601 " - " ASN E 386 " " NAG E 602 " - " ASN E 197 " " NAG E 603 " - " ASN E 355 " " NAG E 604 " - " ASN E 448 " " NAG E 605 " - " ASN E 154 " " NAG E 606 " - " ASN E 234 " " NAG I 601 " - " ASN I 355 " " NAG I 602 " - " ASN I 154 " " NAG I 603 " - " ASN I 448 " " NAG I 604 " - " ASN I 386 " " NAG I 605 " - " ASN I 197 " " NAG I 606 " - " ASN I 234 " " NAG M 1 " - " ASN A 442 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 262 " " NAG P 1 " - " ASN A 362 " " NAG Q 1 " - " ASN A 301 " " NAG R 1 " - " ASN E 442 " " NAG S 1 " - " ASN E 332 " " NAG T 1 " - " ASN E 362 " " NAG U 1 " - " ASN E 301 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN I 332 " " NAG X 1 " - " ASN I 442 " " NAG Y 1 " - " ASN I 392 " " NAG Z 1 " - " ASN I 362 " " NAG a 1 " - " ASN I 262 " " NAG b 1 " - " ASN I 301 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 57 sheets defined 20.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.619A pdb=" N VAL A 65 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS A 66 " --> pdb=" O LYS A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.642A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.694A pdb=" N LYS A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N HIS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.944A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.173A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.696A pdb=" N ILE B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.643A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 664 removed outlier: 3.934A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 139 through 145 removed outlier: 4.005A pdb=" N GLU C 145 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 126 through 132 Processing helix chain 'D' and resid 188 through 193 Processing helix chain 'E' and resid 62 through 67 removed outlier: 3.676A pdb=" N VAL E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS E 66 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.344A pdb=" N ASP E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 117 " --> pdb=" O ASP E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 138 through 151 Processing helix chain 'E' and resid 335 through 353 removed outlier: 4.008A pdb=" N HIS E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.047A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.684A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 542 removed outlier: 4.017A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 597 removed outlier: 3.533A pdb=" N ASP F 589 " --> pdb=" O ARG F 585 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 625 removed outlier: 3.520A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.773A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 664 removed outlier: 3.756A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 139 through 145 removed outlier: 4.043A pdb=" N GLU G 145 " --> pdb=" O SER G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'H' and resid 84 through 88 Processing helix chain 'H' and resid 126 through 132 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.752A pdb=" N ASN I 67 " --> pdb=" O LYS I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 117 removed outlier: 4.407A pdb=" N ASP I 102 " --> pdb=" O ASN I 98 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 126 Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'I' and resid 335 through 351 removed outlier: 3.511A pdb=" N LYS I 351 " --> pdb=" O ILE I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 377 through 381 Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 474 through 484 removed outlier: 4.360A pdb=" N ASN I 478 " --> pdb=" O ASP I 474 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TRP I 479 " --> pdb=" O MET I 475 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 542 Processing helix chain 'J' and resid 570 through 597 Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 618 through 625 removed outlier: 3.546A pdb=" N ILE J 622 " --> pdb=" O ASN J 618 " (cutoff:3.500A) Processing helix chain 'J' and resid 627 through 636 removed outlier: 4.066A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 662 removed outlier: 3.924A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) 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 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 139 through 145 removed outlier: 3.605A pdb=" N GLU K 145 " --> pdb=" O SER K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 170 No H-bonds generated for 'chain 'K' and resid 168 through 170' Processing helix chain 'K' and resid 197 through 201 Processing helix chain 'L' and resid 84 through 88 Processing helix chain 'L' and resid 126 through 131 Processing helix chain 'L' and resid 188 through 193 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 498 removed outlier: 5.264A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.059A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (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 removed outlier: 3.576A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 167 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.618A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 323 removed outlier: 6.819A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN A 417 " --> pdb=" O ASN A 386 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 316 through 323 removed outlier: 6.819A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.996A pdb=" N TYR C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET C 34 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.119A pdb=" N TYR C 188 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.119A pdb=" N TYR C 188 " --> pdb=" O ASP C 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 163 through 166 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.907A pdb=" N LEU D 38 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR D 54 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 13 Processing sheet with id=AB9, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.890A pdb=" N VAL D 138 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TYR D 178 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AC2, first strand: chain 'E' and resid 495 through 498 removed outlier: 5.380A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.115A pdb=" N LEU E 84 " --> pdb=" O THR E 244 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.782A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 167 through 175 Processing sheet with id=AC7, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.576A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.667A pdb=" N GLU E 466 " --> pdb=" O THR E 357 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 316 through 323 removed outlier: 5.318A pdb=" N TYR E 318 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP E 321A" --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN E 300 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE E 443 " --> pdb=" O ASN E 300 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 373 through 375 removed outlier: 4.769A pdb=" N GLN E 417 " --> pdb=" O ASN E 386 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER E 334 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.967A pdb=" N TYR G 33 " --> pdb=" O ASP G 99 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N MET G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.129A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 132 through 136 removed outlier: 6.129A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 162 through 166 removed outlier: 4.412A pdb=" N TYR G 206 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.835A pdb=" N LEU H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR H 54 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP H 40 " --> pdb=" O LEU H 52 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AD9, first strand: chain 'H' and resid 19 through 24 Processing sheet with id=AE1, first strand: chain 'H' and resid 119 through 123 removed outlier: 3.779A pdb=" N VAL H 138 " --> pdb=" O PHE H 123 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TYR H 178 " --> pdb=" O ASN H 143 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN H 165 " --> pdb=" O THR H 183 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 158 through 159 Processing sheet with id=AE3, first strand: chain 'I' and resid 495 through 498 removed outlier: 5.292A pdb=" N VAL J 608 " --> pdb=" O VAL I 36 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N VAL I 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR J 606 " --> pdb=" O VAL I 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 45 through 47 removed outlier: 4.072A pdb=" N LEU I 84 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AE6, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.565A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 93 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY I 237 " --> pdb=" O PHE I 93 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 167 through 175 Processing sheet with id=AE8, first strand: chain 'I' and resid 202 through 203 removed outlier: 6.583A pdb=" N THR I 202 " --> pdb=" O TYR I 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 271 through 273 removed outlier: 7.060A pdb=" N GLU I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER I 334 " --> pdb=" O GLU I 293 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS I 421 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 316 through 323 removed outlier: 6.827A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N ILE I 284 " --> pdb=" O ASP I 457 " (cutoff:3.500A) removed outlier: 11.311A pdb=" N ASP I 457 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N VAL I 286 " --> pdb=" O THR I 455 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N THR I 455 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N LEU I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 11.809A pdb=" N LEU I 453 " --> pdb=" O LEU I 288 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY I 451 " --> pdb=" O THR I 290 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL I 292 " --> pdb=" O ILE I 449 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN I 300 " --> pdb=" O GLY I 441 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY I 441 " --> pdb=" O ASN I 300 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU I 466 " --> pdb=" O THR I 357 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'K' and resid 11 through 12 removed outlier: 5.056A pdb=" N TYR K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.147A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.147A pdb=" N TYR K 188 " --> pdb=" O ASP K 156 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 162 through 166 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.046A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.046A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.968A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 158 through 159 1002 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.53 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5937 1.33 - 1.45: 5234 1.45 - 1.57: 14236 1.57 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 25587 Sorted by residual: bond pdb=" C5 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.413 1.491 -0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C3 BMA W 3 " pdb=" O3 BMA W 3 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.413 1.490 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 25582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 31988 3.34 - 6.68: 2747 6.68 - 10.02: 64 10.02 - 13.36: 8 13.36 - 16.69: 4 Bond angle restraints: 34811 Sorted by residual: angle pdb=" N THR E 450 " pdb=" CA THR E 450 " pdb=" C THR E 450 " ideal model delta sigma weight residual 110.80 127.49 -16.69 2.13e+00 2.20e-01 6.14e+01 angle pdb=" N ARG A 446 " pdb=" CA ARG A 446 " pdb=" C ARG A 446 " ideal model delta sigma weight residual 109.72 122.22 -12.50 1.60e+00 3.91e-01 6.10e+01 angle pdb=" CA PHE F 519 " pdb=" CB PHE F 519 " pdb=" CG PHE F 519 " ideal model delta sigma weight residual 113.80 121.48 -7.68 1.00e+00 1.00e+00 5.90e+01 angle pdb=" N THR I 450 " pdb=" CA THR I 450 " pdb=" C THR I 450 " ideal model delta sigma weight residual 110.80 127.04 -16.24 2.13e+00 2.20e-01 5.81e+01 angle pdb=" CA PHE B 519 " pdb=" CB PHE B 519 " pdb=" CG PHE B 519 " ideal model delta sigma weight residual 113.80 121.32 -7.52 1.00e+00 1.00e+00 5.66e+01 ... (remaining 34806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13589 17.99 - 35.97: 1038 35.97 - 53.96: 154 53.96 - 71.94: 37 71.94 - 89.93: 35 Dihedral angle restraints: 14853 sinusoidal: 5874 harmonic: 8979 Sorted by residual: dihedral pdb=" C ARG A 446 " pdb=" N ARG A 446 " pdb=" CA ARG A 446 " pdb=" CB ARG A 446 " ideal model delta harmonic sigma weight residual -122.60 -149.65 27.05 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N ARG A 446 " pdb=" C ARG A 446 " pdb=" CA ARG A 446 " pdb=" CB ARG A 446 " ideal model delta harmonic sigma weight residual 122.80 148.98 -26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual 93.00 170.00 -77.00 1 1.00e+01 1.00e-02 7.44e+01 ... (remaining 14850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 4047 0.277 - 0.554: 52 0.554 - 0.831: 4 0.831 - 1.109: 6 1.109 - 1.386: 10 Chirality restraints: 4119 Sorted by residual: chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-02 2.50e+03 4.80e+03 chirality pdb=" C1 BMA V 3 " pdb=" O4 NAG V 2 " pdb=" C2 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-02 2.50e+03 4.72e+03 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.03 -1.37 2.00e-02 2.50e+03 4.72e+03 ... (remaining 4116 not shown) Planarity restraints: 4410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 623 " -0.268 2.00e-02 2.50e+03 1.36e-01 4.61e+02 pdb=" CG TRP F 623 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 623 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP F 623 " 0.127 2.00e-02 2.50e+03 pdb=" NE1 TRP F 623 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP F 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP F 623 " 0.177 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 623 " -0.169 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 623 " 0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP F 623 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 623 " -0.234 2.00e-02 2.50e+03 1.19e-01 3.56e+02 pdb=" CG TRP J 623 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP J 623 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP J 623 " 0.118 2.00e-02 2.50e+03 pdb=" NE1 TRP J 623 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TRP J 623 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP J 623 " 0.160 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 623 " -0.137 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 623 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP J 623 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 623 " 0.231 2.00e-02 2.50e+03 1.18e-01 3.47e+02 pdb=" CG TRP B 623 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP B 623 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP B 623 " -0.111 2.00e-02 2.50e+03 pdb=" NE1 TRP B 623 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP B 623 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 623 " -0.163 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 623 " 0.135 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 623 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 623 " 0.126 2.00e-02 2.50e+03 ... (remaining 4407 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 12276 2.98 - 3.46: 24784 3.46 - 3.94: 41683 3.94 - 4.42: 45741 4.42 - 4.90: 76933 Nonbonded interactions: 201417 Sorted by model distance: nonbonded pdb=" O2 MAN N 4 " pdb=" O3 MAN N 4 " model vdw 2.498 2.432 nonbonded pdb=" OD1 ASP D 175 " pdb=" OG1 THR D 177 " model vdw 2.526 3.040 nonbonded pdb=" OD1 ASP H 175 " pdb=" OG1 THR H 177 " model vdw 2.547 3.040 nonbonded pdb=" OG SER H 10 " pdb=" OE2 GLU H 110 " model vdw 2.548 3.040 nonbonded pdb=" OD2 ASP K 113 " pdb=" O4 MAN W 5 " model vdw 2.550 3.040 ... (remaining 201412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'a' } 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 group one per residue 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.960 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- 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 : 0.014 0.078 25704 Z= 0.798 Angle : 1.961 16.694 35114 Z= 1.242 Chirality : 0.131 1.386 4119 Planarity : 0.016 0.151 4376 Dihedral : 13.919 89.930 8949 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.18 Ramachandran Plot: Outliers : 1.33 % Allowed : 7.63 % Favored : 91.03 % Rotamer: Outliers : 1.03 % Allowed : 3.94 % Favored : 95.03 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.25 (0.15), residues: 3078 helix: -1.83 (0.19), residues: 435 sheet: -0.39 (0.18), residues: 813 loop : -0.73 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG G 56 TYR 0.152 0.022 TYR E 400 PHE 0.114 0.018 PHE K 27 TRP 0.268 0.029 TRP F 623 HIS 0.036 0.006 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.01371 / 0.80 (25587) covalent geometry : angle 1.91486 / 1.24 (34811) SS BOND : bond 0.00610 / 0.43 ( 48) SS BOND : angle 2.41733 / 1.60 ( 96) hydrogen bonds : bond 0.16093 / 10.79 ( 934) hydrogen bonds : angle 9.21406 / 6.36 ( 2574) link_ALPHA1-3 : bond 0.02526 / 1.46 ( 6) link_ALPHA1-3 : angle 7.78590 / 5.19 ( 18) link_ALPHA1-6 : bond 0.01665 / 0.82 ( 6) link_ALPHA1-6 : angle 5.10062 / 2.95 ( 18) link_BETA1-4 : bond 0.02653 / 1.73 ( 23) link_BETA1-4 : angle 6.82216 / 4.59 ( 69) link_NAG-ASN : bond 0.01110 / 0.71 ( 34) link_NAG-ASN : angle 4.47225 / 2.93 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.8470 (mtp) cc_final: 0.8110 (mtp) REVERT: C 213 LYS cc_start: 0.9524 (mmtt) cc_final: 0.9232 (mmtm) REVERT: E 66 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6637 (p-80) REVERT: E 151 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: F 530 MET cc_start: 0.8571 (mtp) cc_final: 0.8237 (mtp) REVERT: G 213 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8977 (mmtm) REVERT: J 530 MET cc_start: 0.8294 (mtp) cc_final: 0.8036 (mtp) REVERT: K 218 LYS cc_start: 0.9104 (pttt) cc_final: 0.8766 (tttp) outliers start: 28 outliers final: 3 residues processed: 116 average time/residue: 0.2187 time to fit residues: 37.7414 Evaluate side-chains 62 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 504 ARG Chi-restraints excluded: chain F residue 540 GLN Chi-restraints excluded: chain I residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.040849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.030834 restraints weight = 249418.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031629 restraints weight = 142171.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.032127 restraints weight = 102752.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.032401 restraints weight = 84835.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.032591 restraints weight = 76165.564| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25704 Z= 0.159 Angle : 0.819 12.523 35114 Z= 0.417 Chirality : 0.049 0.234 4119 Planarity : 0.004 0.051 4376 Dihedral : 7.381 60.184 3370 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.13 % Favored : 94.41 % Rotamer: Outliers : 0.85 % Allowed : 5.93 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.56 (0.15), residues: 3078 helix: 0.05 (0.24), residues: 471 sheet: -0.29 (0.17), residues: 927 loop : -0.45 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 500 TYR 0.017 0.002 TYR I 61 PHE 0.018 0.002 PHE A 376 TRP 0.034 0.003 TRP I 112 HIS 0.009 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (25587) covalent geometry : angle 0.79039 / 0.41 (34811) SS BOND : bond 0.00236 / 0.16 ( 48) SS BOND : angle 0.90582 / 0.56 ( 96) hydrogen bonds : bond 0.05231 / 3.50 ( 934) hydrogen bonds : angle 6.93402 / 4.81 ( 2574) link_ALPHA1-3 : bond 0.01285 / 0.72 ( 6) link_ALPHA1-3 : angle 3.80078 / 2.34 ( 18) link_ALPHA1-6 : bond 0.01190 / 0.71 ( 6) link_ALPHA1-6 : angle 1.72183 / 0.94 ( 18) link_BETA1-4 : bond 0.01285 / 0.91 ( 23) link_BETA1-4 : angle 3.30200 / 2.50 ( 69) link_NAG-ASN : bond 0.00448 / 0.31 ( 34) link_NAG-ASN : angle 2.53897 / 1.70 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 VAL cc_start: 0.5564 (OUTLIER) cc_final: 0.5204 (p) REVERT: C 213 LYS cc_start: 0.9592 (mmtt) cc_final: 0.9261 (mmtm) REVERT: C 218 LYS cc_start: 0.9217 (pttt) cc_final: 0.8753 (tttp) REVERT: E 151 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7806 (mm-30) REVERT: E 417 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: F 530 MET cc_start: 0.8315 (mtp) cc_final: 0.7958 (mtp) REVERT: G 213 LYS cc_start: 0.9434 (mmtt) cc_final: 0.9040 (mmtm) REVERT: G 218 LYS cc_start: 0.9243 (pttt) cc_final: 0.8918 (tttp) REVERT: J 614 TRP cc_start: 0.6174 (OUTLIER) cc_final: 0.5702 (m-10) outliers start: 23 outliers final: 5 residues processed: 82 average time/residue: 0.1950 time to fit residues: 25.5070 Evaluate side-chains 66 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 614 TRP Chi-restraints excluded: chain K residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 35 optimal weight: 6.9990 chunk 158 optimal weight: 0.0060 chunk 56 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 291 optimal weight: 40.0000 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS A 404 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.040006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.029851 restraints weight = 251912.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.030625 restraints weight = 146064.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.031115 restraints weight = 106469.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031404 restraints weight = 88183.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.031571 restraints weight = 79051.110| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25704 Z= 0.217 Angle : 0.774 11.062 35114 Z= 0.383 Chirality : 0.048 0.269 4119 Planarity : 0.005 0.053 4376 Dihedral : 6.515 47.473 3361 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.59 % Favored : 94.09 % Rotamer: Outliers : 1.22 % Allowed : 6.56 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.53 (0.16), residues: 3078 helix: 0.48 (0.25), residues: 483 sheet: -0.28 (0.16), residues: 996 loop : -0.56 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 617 TYR 0.021 0.002 TYR A 61 PHE 0.020 0.002 PHE A 376 TRP 0.023 0.002 TRP I 112 HIS 0.008 0.002 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 (25587) covalent geometry : angle 0.74919 / 0.38 (34811) SS BOND : bond 0.00300 / 0.21 ( 48) SS BOND : angle 1.00181 / 0.61 ( 96) hydrogen bonds : bond 0.04428 / 2.97 ( 934) hydrogen bonds : angle 6.35315 / 4.41 ( 2574) link_ALPHA1-3 : bond 0.00420 / 0.24 ( 6) link_ALPHA1-3 : angle 3.57106 / 2.12 ( 18) link_ALPHA1-6 : bond 0.00465 / 0.23 ( 6) link_ALPHA1-6 : angle 2.11110 / 1.13 ( 18) link_BETA1-4 : bond 0.01111 / 0.78 ( 23) link_BETA1-4 : angle 2.88637 / 2.17 ( 69) link_NAG-ASN : bond 0.00478 / 0.27 ( 34) link_NAG-ASN : angle 2.24271 / 1.48 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9592 (mmtt) cc_final: 0.9246 (mmtm) REVERT: E 135 THR cc_start: 0.3995 (OUTLIER) cc_final: 0.3692 (p) REVERT: E 417 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: F 530 MET cc_start: 0.8540 (mtp) cc_final: 0.8199 (mtp) REVERT: G 213 LYS cc_start: 0.9456 (mmtt) cc_final: 0.9060 (mmtm) REVERT: G 218 LYS cc_start: 0.9218 (pttt) cc_final: 0.8898 (tttp) REVERT: I 135 THR cc_start: 0.3832 (OUTLIER) cc_final: 0.3538 (p) REVERT: J 540 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7834 (tp40) REVERT: K 218 LYS cc_start: 0.9197 (pttt) cc_final: 0.8787 (tptt) outliers start: 33 outliers final: 11 residues processed: 88 average time/residue: 0.1766 time to fit residues: 25.7708 Evaluate side-chains 71 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain H residue 195 ASN Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN G 52 ASN ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 315 GLN I 350 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.039218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029120 restraints weight = 251304.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.029855 restraints weight = 146739.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.030308 restraints weight = 108068.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.030594 restraints weight = 90485.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.030729 restraints weight = 81069.520| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 25704 Z= 0.326 Angle : 0.857 11.332 35114 Z= 0.419 Chirality : 0.050 0.238 4119 Planarity : 0.005 0.056 4376 Dihedral : 6.658 53.478 3361 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.47 % Favored : 93.24 % Rotamer: Outliers : 1.29 % Allowed : 8.21 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.80 (0.15), residues: 3078 helix: 0.40 (0.25), residues: 483 sheet: -0.51 (0.16), residues: 996 loop : -0.75 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.021 0.002 TYR E 61 PHE 0.026 0.003 PHE E 376 TRP 0.024 0.003 TRP I 112 HIS 0.010 0.003 HIS I 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.33 (25587) covalent geometry : angle 0.83178 / 0.41 (34811) SS BOND : bond 0.00412 / 0.27 ( 48) SS BOND : angle 1.13841 / 0.71 ( 96) hydrogen bonds : bond 0.04785 / 3.21 ( 934) hydrogen bonds : angle 6.46934 / 4.48 ( 2574) link_ALPHA1-3 : bond 0.00337 / 0.15 ( 6) link_ALPHA1-3 : angle 3.90001 / 2.23 ( 18) link_ALPHA1-6 : bond 0.00348 / 0.18 ( 6) link_ALPHA1-6 : angle 2.69689 / 1.43 ( 18) link_BETA1-4 : bond 0.01142 / 0.76 ( 23) link_BETA1-4 : angle 2.90573 / 2.16 ( 69) link_NAG-ASN : bond 0.00673 / 0.39 ( 34) link_NAG-ASN : angle 2.38325 / 1.56 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9583 (mmtt) cc_final: 0.9221 (mppt) REVERT: E 135 THR cc_start: 0.3989 (OUTLIER) cc_final: 0.3696 (p) REVERT: E 417 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: F 530 MET cc_start: 0.8513 (mtp) cc_final: 0.7970 (mtp) REVERT: F 626 MET cc_start: 0.8513 (ttm) cc_final: 0.8246 (ttm) REVERT: G 213 LYS cc_start: 0.9482 (mmtt) cc_final: 0.9051 (mmtm) REVERT: G 218 LYS cc_start: 0.9242 (pttt) cc_final: 0.8817 (tttp) REVERT: I 467 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7832 (p) REVERT: K 218 LYS cc_start: 0.9215 (pttt) cc_final: 0.8784 (tptt) outliers start: 35 outliers final: 18 residues processed: 86 average time/residue: 0.1655 time to fit residues: 23.6497 Evaluate side-chains 76 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 141 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 289 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 204 GLN I 404 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.040332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.030269 restraints weight = 251874.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.031080 restraints weight = 144142.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031587 restraints weight = 103998.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.031895 restraints weight = 85855.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.032084 restraints weight = 76425.822| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25704 Z= 0.111 Angle : 0.653 9.740 35114 Z= 0.322 Chirality : 0.044 0.215 4119 Planarity : 0.004 0.056 4376 Dihedral : 5.906 53.963 3361 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.13 % Favored : 94.57 % Rotamer: Outliers : 0.70 % Allowed : 8.84 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.37 (0.16), residues: 3078 helix: 1.33 (0.26), residues: 456 sheet: -0.38 (0.16), residues: 1023 loop : -0.54 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 216 TYR 0.019 0.001 TYR I 61 PHE 0.016 0.001 PHE A 376 TRP 0.019 0.002 TRP K 106 HIS 0.008 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (25587) covalent geometry : angle 0.63066 / 0.32 (34811) SS BOND : bond 0.00217 / 0.14 ( 48) SS BOND : angle 0.76079 / 0.48 ( 96) hydrogen bonds : bond 0.03555 / 2.40 ( 934) hydrogen bonds : angle 5.75000 / 3.97 ( 2574) link_ALPHA1-3 : bond 0.00763 / 0.37 ( 6) link_ALPHA1-3 : angle 3.44192 / 2.10 ( 18) link_ALPHA1-6 : bond 0.00779 / 0.48 ( 6) link_ALPHA1-6 : angle 1.51760 / 0.85 ( 18) link_BETA1-4 : bond 0.00952 / 0.69 ( 23) link_BETA1-4 : angle 2.67138 / 2.01 ( 69) link_NAG-ASN : bond 0.00209 / 0.14 ( 34) link_NAG-ASN : angle 1.77455 / 1.12 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6695 (tm-30) REVERT: B 626 MET cc_start: 0.8371 (ttt) cc_final: 0.8065 (ttt) REVERT: C 34 MET cc_start: 0.9093 (mmm) cc_final: 0.8864 (mmm) REVERT: C 213 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9200 (mmtm) REVERT: F 530 MET cc_start: 0.8629 (mtp) cc_final: 0.8239 (mtp) REVERT: G 34 MET cc_start: 0.9213 (mmm) cc_final: 0.8961 (mmm) REVERT: G 213 LYS cc_start: 0.9471 (mmtt) cc_final: 0.9018 (mmtm) REVERT: J 614 TRP cc_start: 0.6225 (OUTLIER) cc_final: 0.5585 (m-10) REVERT: K 218 LYS cc_start: 0.9220 (pttt) cc_final: 0.8801 (tptt) outliers start: 19 outliers final: 8 residues processed: 76 average time/residue: 0.1734 time to fit residues: 21.7514 Evaluate side-chains 64 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 614 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 155 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 77 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 169 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.039816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.029699 restraints weight = 253155.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.030494 restraints weight = 146786.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.030990 restraints weight = 106767.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.031266 restraints weight = 88045.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031478 restraints weight = 79028.929| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25704 Z= 0.172 Angle : 0.672 10.245 35114 Z= 0.328 Chirality : 0.045 0.221 4119 Planarity : 0.004 0.055 4376 Dihedral : 5.841 55.901 3361 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.82 % Favored : 93.92 % Rotamer: Outliers : 0.81 % Allowed : 9.36 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.41 (0.16), residues: 3078 helix: 1.31 (0.26), residues: 465 sheet: -0.47 (0.16), residues: 1035 loop : -0.52 (0.17), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 216 TYR 0.020 0.002 TYR L 92 PHE 0.018 0.002 PHE E 376 TRP 0.015 0.002 TRP I 112 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (25587) covalent geometry : angle 0.64890 / 0.32 (34811) SS BOND : bond 0.00271 / 0.18 ( 48) SS BOND : angle 0.77722 / 0.49 ( 96) hydrogen bonds : bond 0.03640 / 2.45 ( 934) hydrogen bonds : angle 5.71871 / 3.93 ( 2574) link_ALPHA1-3 : bond 0.00402 / 0.20 ( 6) link_ALPHA1-3 : angle 3.48132 / 2.04 ( 18) link_ALPHA1-6 : bond 0.00454 / 0.27 ( 6) link_ALPHA1-6 : angle 1.76241 / 0.98 ( 18) link_BETA1-4 : bond 0.00989 / 0.70 ( 23) link_BETA1-4 : angle 2.64627 / 1.98 ( 69) link_NAG-ASN : bond 0.00353 / 0.21 ( 34) link_NAG-ASN : angle 1.88743 / 1.22 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 626 MET cc_start: 0.8424 (ttt) cc_final: 0.8187 (ttt) REVERT: C 34 MET cc_start: 0.9132 (mmm) cc_final: 0.8911 (mmm) REVERT: C 213 LYS cc_start: 0.9589 (mmtt) cc_final: 0.9206 (mmtm) REVERT: F 530 MET cc_start: 0.8571 (mtp) cc_final: 0.8129 (mtp) REVERT: G 34 MET cc_start: 0.9226 (mmm) cc_final: 0.8804 (mmm) REVERT: G 213 LYS cc_start: 0.9483 (mmtt) cc_final: 0.9030 (mmtm) REVERT: K 218 LYS cc_start: 0.9213 (pttt) cc_final: 0.8786 (tptt) outliers start: 22 outliers final: 13 residues processed: 74 average time/residue: 0.1551 time to fit residues: 19.2412 Evaluate side-chains 67 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 248 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 235 optimal weight: 0.4980 chunk 162 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 110 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.039946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.029885 restraints weight = 253816.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.030659 restraints weight = 145558.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031165 restraints weight = 105717.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031473 restraints weight = 87166.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031654 restraints weight = 77558.264| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25704 Z= 0.131 Angle : 0.635 9.929 35114 Z= 0.311 Chirality : 0.044 0.213 4119 Planarity : 0.004 0.052 4376 Dihedral : 5.664 57.301 3361 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.56 % Favored : 94.18 % Rotamer: Outliers : 0.74 % Allowed : 9.50 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 3078 helix: 1.39 (0.26), residues: 465 sheet: -0.41 (0.15), residues: 1074 loop : -0.42 (0.17), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 216 TYR 0.019 0.001 TYR I 61 PHE 0.018 0.001 PHE A 376 TRP 0.018 0.001 TRP I 427 HIS 0.007 0.001 HIS I 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (25587) covalent geometry : angle 0.61351 / 0.31 (34811) SS BOND : bond 0.00234 / 0.16 ( 48) SS BOND : angle 0.69263 / 0.44 ( 96) hydrogen bonds : bond 0.03422 / 2.31 ( 934) hydrogen bonds : angle 5.56753 / 3.83 ( 2574) link_ALPHA1-3 : bond 0.00509 / 0.23 ( 6) link_ALPHA1-3 : angle 3.41423 / 2.04 ( 18) link_ALPHA1-6 : bond 0.00593 / 0.36 ( 6) link_ALPHA1-6 : angle 1.57991 / 0.89 ( 18) link_BETA1-4 : bond 0.00939 / 0.67 ( 23) link_BETA1-4 : angle 2.58473 / 1.94 ( 69) link_NAG-ASN : bond 0.00241 / 0.16 ( 34) link_NAG-ASN : angle 1.75377 / 1.12 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6632 (tm-30) REVERT: C 213 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9204 (mmtm) REVERT: C 218 LYS cc_start: 0.9189 (pttt) cc_final: 0.8717 (tptt) REVERT: F 530 MET cc_start: 0.8550 (mtp) cc_final: 0.8134 (mtp) REVERT: G 34 MET cc_start: 0.9200 (mmm) cc_final: 0.8989 (mmm) REVERT: G 213 LYS cc_start: 0.9492 (mmtt) cc_final: 0.9039 (mmtm) REVERT: I 213 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8843 (tp) REVERT: K 34 MET cc_start: 0.9034 (mmm) cc_final: 0.8753 (mmm) REVERT: K 218 LYS cc_start: 0.9187 (pttt) cc_final: 0.8765 (tptt) outliers start: 20 outliers final: 16 residues processed: 74 average time/residue: 0.1630 time to fit residues: 19.7930 Evaluate side-chains 72 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 236 optimal weight: 0.9980 chunk 303 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 203 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 4 optimal weight: 30.0000 chunk 243 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.040042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.029974 restraints weight = 251408.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.030782 restraints weight = 140679.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.031296 restraints weight = 100608.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.031606 restraints weight = 82624.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.031802 restraints weight = 73382.686| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25704 Z= 0.115 Angle : 0.615 9.718 35114 Z= 0.301 Chirality : 0.044 0.212 4119 Planarity : 0.004 0.049 4376 Dihedral : 5.483 58.556 3361 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.43 % Favored : 94.31 % Rotamer: Outliers : 0.88 % Allowed : 9.47 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.23 (0.16), residues: 3078 helix: 1.50 (0.25), residues: 465 sheet: -0.35 (0.15), residues: 1092 loop : -0.41 (0.18), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 216 TYR 0.019 0.001 TYR L 92 PHE 0.017 0.001 PHE A 376 TRP 0.015 0.001 TRP K 106 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (25587) covalent geometry : angle 0.59360 / 0.30 (34811) SS BOND : bond 0.00225 / 0.15 ( 48) SS BOND : angle 0.64471 / 0.41 ( 96) hydrogen bonds : bond 0.03189 / 2.15 ( 934) hydrogen bonds : angle 5.40630 / 3.71 ( 2574) link_ALPHA1-3 : bond 0.00578 / 0.27 ( 6) link_ALPHA1-3 : angle 3.35809 / 2.01 ( 18) link_ALPHA1-6 : bond 0.00626 / 0.38 ( 6) link_ALPHA1-6 : angle 1.45522 / 0.84 ( 18) link_BETA1-4 : bond 0.00934 / 0.67 ( 23) link_BETA1-4 : angle 2.55850 / 1.91 ( 69) link_NAG-ASN : bond 0.00214 / 0.14 ( 34) link_NAG-ASN : angle 1.67221 / 1.06 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6579 (tm-30) REVERT: C 213 LYS cc_start: 0.9584 (mmtt) cc_final: 0.9197 (mmtm) REVERT: C 218 LYS cc_start: 0.9211 (pttt) cc_final: 0.8745 (tptt) REVERT: F 530 MET cc_start: 0.8560 (mtp) cc_final: 0.8153 (mtp) REVERT: G 213 LYS cc_start: 0.9497 (mmtt) cc_final: 0.9044 (mmtm) REVERT: G 218 LYS cc_start: 0.9246 (pttt) cc_final: 0.8811 (tptt) REVERT: I 213 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8826 (tp) REVERT: J 614 TRP cc_start: 0.6155 (OUTLIER) cc_final: 0.5492 (m-90) REVERT: K 34 MET cc_start: 0.9110 (mmm) cc_final: 0.8825 (mmm) REVERT: K 218 LYS cc_start: 0.9206 (pttt) cc_final: 0.8761 (tptt) outliers start: 24 outliers final: 16 residues processed: 74 average time/residue: 0.1580 time to fit residues: 19.4392 Evaluate side-chains 75 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 614 TRP Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 36 optimal weight: 40.0000 chunk 207 optimal weight: 6.9990 chunk 282 optimal weight: 0.0570 chunk 61 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 253 optimal weight: 0.1980 chunk 200 optimal weight: 20.0000 overall best weight: 3.0504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.039793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.029752 restraints weight = 254682.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.030534 restraints weight = 145753.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.031026 restraints weight = 105995.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.031318 restraints weight = 87670.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.031485 restraints weight = 78391.888| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25704 Z= 0.153 Angle : 0.635 9.917 35114 Z= 0.310 Chirality : 0.044 0.214 4119 Planarity : 0.004 0.046 4376 Dihedral : 5.502 58.691 3360 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.59 % Favored : 94.15 % Rotamer: Outliers : 0.77 % Allowed : 9.61 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.16), residues: 3078 helix: 1.52 (0.26), residues: 465 sheet: -0.32 (0.15), residues: 1086 loop : -0.40 (0.18), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 476 TYR 0.017 0.001 TYR E 61 PHE 0.017 0.001 PHE A 376 TRP 0.014 0.002 TRP E 112 HIS 0.006 0.001 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (25587) covalent geometry : angle 0.61299 / 0.31 (34811) SS BOND : bond 0.00257 / 0.18 ( 48) SS BOND : angle 0.69532 / 0.44 ( 96) hydrogen bonds : bond 0.03312 / 2.22 ( 934) hydrogen bonds : angle 5.42004 / 3.72 ( 2574) link_ALPHA1-3 : bond 0.00427 / 0.20 ( 6) link_ALPHA1-3 : angle 3.39695 / 1.99 ( 18) link_ALPHA1-6 : bond 0.00437 / 0.25 ( 6) link_ALPHA1-6 : angle 1.62438 / 0.92 ( 18) link_BETA1-4 : bond 0.00946 / 0.67 ( 23) link_BETA1-4 : angle 2.58715 / 1.92 ( 69) link_NAG-ASN : bond 0.00315 / 0.19 ( 34) link_NAG-ASN : angle 1.75583 / 1.12 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.6619 (tm-30) REVERT: C 213 LYS cc_start: 0.9555 (mmtt) cc_final: 0.9187 (mmtm) REVERT: C 218 LYS cc_start: 0.9226 (pttt) cc_final: 0.8758 (tptt) REVERT: F 530 MET cc_start: 0.8556 (mtp) cc_final: 0.8133 (mtp) REVERT: G 213 LYS cc_start: 0.9460 (mmtt) cc_final: 0.9008 (mmtm) REVERT: G 218 LYS cc_start: 0.9245 (pttt) cc_final: 0.8794 (tptt) REVERT: I 213 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8914 (tp) REVERT: K 34 MET cc_start: 0.9073 (mmm) cc_final: 0.8799 (mmm) REVERT: K 218 LYS cc_start: 0.9209 (pttt) cc_final: 0.8763 (tptt) outliers start: 21 outliers final: 17 residues processed: 73 average time/residue: 0.1683 time to fit residues: 20.7483 Evaluate side-chains 75 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 75 optimal weight: 0.0970 chunk 279 optimal weight: 8.9990 chunk 115 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 250 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 174 optimal weight: 7.9990 chunk 246 optimal weight: 0.8980 chunk 238 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN L 96 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.040317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.030332 restraints weight = 252422.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.031154 restraints weight = 140058.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.031671 restraints weight = 100063.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.031987 restraints weight = 81813.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.032169 restraints weight = 72423.884| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 25704 Z= 0.095 Angle : 0.586 9.373 35114 Z= 0.287 Chirality : 0.043 0.205 4119 Planarity : 0.004 0.044 4376 Dihedral : 5.229 59.791 3360 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.10 % Favored : 94.61 % Rotamer: Outliers : 0.63 % Allowed : 9.72 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.08 (0.16), residues: 3078 helix: 1.75 (0.26), residues: 462 sheet: -0.31 (0.16), residues: 1062 loop : -0.32 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 216 TYR 0.018 0.001 TYR G 33 PHE 0.016 0.001 PHE A 376 TRP 0.015 0.001 TRP K 106 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.09 (25587) covalent geometry : angle 0.56517 / 0.28 (34811) SS BOND : bond 0.00200 / 0.14 ( 48) SS BOND : angle 0.60939 / 0.40 ( 96) hydrogen bonds : bond 0.02899 / 1.95 ( 934) hydrogen bonds : angle 5.17219 / 3.55 ( 2574) link_ALPHA1-3 : bond 0.00764 / 0.35 ( 6) link_ALPHA1-3 : angle 3.25753 / 1.97 ( 18) link_ALPHA1-6 : bond 0.00735 / 0.45 ( 6) link_ALPHA1-6 : angle 1.35223 / 0.80 ( 18) link_BETA1-4 : bond 0.00923 / 0.66 ( 23) link_BETA1-4 : angle 2.55663 / 1.91 ( 69) link_NAG-ASN : bond 0.00198 / 0.14 ( 34) link_NAG-ASN : angle 1.52135 / 0.94 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: C 213 LYS cc_start: 0.9578 (mmtt) cc_final: 0.9187 (mmtm) REVERT: C 218 LYS cc_start: 0.9205 (pttt) cc_final: 0.8740 (tptt) REVERT: F 530 MET cc_start: 0.8570 (mtp) cc_final: 0.8193 (mtp) REVERT: G 213 LYS cc_start: 0.9479 (mmtt) cc_final: 0.9045 (mmtm) REVERT: G 218 LYS cc_start: 0.9254 (pttt) cc_final: 0.8813 (tptt) REVERT: I 213 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8904 (tp) REVERT: J 614 TRP cc_start: 0.5998 (OUTLIER) cc_final: 0.5238 (m-90) REVERT: K 34 MET cc_start: 0.9134 (mmm) cc_final: 0.8919 (mmm) REVERT: K 218 LYS cc_start: 0.9182 (pttt) cc_final: 0.8726 (tptt) outliers start: 17 outliers final: 12 residues processed: 74 average time/residue: 0.1800 time to fit residues: 21.8660 Evaluate side-chains 72 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain J residue 614 TRP Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 197 optimal weight: 0.0040 chunk 285 optimal weight: 0.3980 chunk 124 optimal weight: 7.9990 chunk 189 optimal weight: 20.0000 overall best weight: 4.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN C 204 GLN D 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.039514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.029460 restraints weight = 253364.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.030226 restraints weight = 145889.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.030711 restraints weight = 106535.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.030991 restraints weight = 88366.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031170 restraints weight = 79217.180| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 25704 Z= 0.215 Angle : 0.684 10.185 35114 Z= 0.332 Chirality : 0.045 0.219 4119 Planarity : 0.004 0.045 4376 Dihedral : 5.491 59.714 3360 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 0.59 % Allowed : 9.94 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.17 (0.16), residues: 3078 helix: 1.47 (0.26), residues: 468 sheet: -0.32 (0.16), residues: 1098 loop : -0.35 (0.18), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 44 TYR 0.018 0.002 TYR E 61 PHE 0.018 0.002 PHE E 376 TRP 0.015 0.002 TRP I 479 HIS 0.006 0.002 HIS E 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.21 (25587) covalent geometry : angle 0.66171 / 0.33 (34811) SS BOND : bond 0.00317 / 0.21 ( 48) SS BOND : angle 0.80662 / 0.52 ( 96) hydrogen bonds : bond 0.03498 / 2.35 ( 934) hydrogen bonds : angle 5.41754 / 3.72 ( 2574) link_ALPHA1-3 : bond 0.00347 / 0.16 ( 6) link_ALPHA1-3 : angle 3.39637 / 1.92 ( 18) link_ALPHA1-6 : bond 0.00276 / 0.14 ( 6) link_ALPHA1-6 : angle 1.89575 / 1.07 ( 18) link_BETA1-4 : bond 0.00994 / 0.69 ( 23) link_BETA1-4 : angle 2.67063 / 1.96 ( 69) link_NAG-ASN : bond 0.00472 / 0.28 ( 34) link_NAG-ASN : angle 1.90546 / 1.23 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4153.71 seconds wall clock time: 72 minutes 57.61 seconds (4377.61 seconds total)