Starting phenix.real_space_refine on Mon Aug 25 04:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_27624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_27624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_27624.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_27624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dow_27624/08_2025/8dow_27624.map" } 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-2.0-5787/lib/python3.9/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 dihedrals: 6 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 dihedrals: 18 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 dihedrals: 12 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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 dihedrals: 9 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 dihedrals: 18 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 dihedrals: 18 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 4.66, per 1000 atoms: 0.19 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: 1.81 Conformation dependent library (CDL) restraints added in 812.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.90 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: 4.34 Time building geometry restraints manager: 2.49 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 - 22.31: 15281 22.31 - 44.63: 769 44.63 - 66.94: 114 66.94 - 89.25: 75 89.25 - 111.57: 25 Dihedral angle restraints: 16264 sinusoidal: 7285 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 16261 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: 2.040 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.650 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 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 : 15.275 111.568 10360 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 aren 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 covalent geometry : bond 0.01371 (25587) covalent geometry : angle 1.91486 (34811) SS BOND : bond 0.00610 ( 48) SS BOND : angle 2.41733 ( 96) hydrogen bonds : bond 0.16093 ( 934) hydrogen bonds : angle 9.21406 ( 2574) link_ALPHA1-3 : bond 0.02526 ( 6) link_ALPHA1-3 : angle 7.78590 ( 18) link_ALPHA1-6 : bond 0.01665 ( 6) link_ALPHA1-6 : angle 5.10062 ( 18) link_BETA1-4 : bond 0.02653 ( 23) link_BETA1-4 : angle 6.82216 ( 69) link_NAG-ASN : bond 0.01110 ( 34) link_NAG-ASN : angle 4.47225 ( 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 : 0.595 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: 0.1950 time to fit residues: 33.6140 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 : 0.794 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 176 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.040873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.030884 restraints weight = 248535.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.031689 restraints weight = 141256.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.032183 restraints weight = 101900.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.032487 restraints weight = 84095.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.032668 restraints weight = 74853.645| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25704 Z= 0.153 Angle : 0.817 13.262 35114 Z= 0.413 Chirality : 0.049 0.333 4119 Planarity : 0.004 0.052 4376 Dihedral : 11.084 75.874 4781 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.00 % Favored : 94.57 % Rotamer: Outliers : 0.85 % Allowed : 5.89 % Favored : 93.26 % 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 aren not related in a simple way. whole: -0.56 (0.15), residues: 3078 helix: 0.10 (0.24), residues: 471 sheet: -0.30 (0.17), residues: 948 loop : -0.46 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 28 TYR 0.018 0.002 TYR A 61 PHE 0.018 0.002 PHE A 233 TRP 0.031 0.003 TRP I 112 HIS 0.009 0.002 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00313 (25587) covalent geometry : angle 0.78271 (34811) SS BOND : bond 0.00333 ( 48) SS BOND : angle 0.88881 ( 96) hydrogen bonds : bond 0.05066 ( 934) hydrogen bonds : angle 6.90808 ( 2574) link_ALPHA1-3 : bond 0.00924 ( 6) link_ALPHA1-3 : angle 4.44120 ( 18) link_ALPHA1-6 : bond 0.01246 ( 6) link_ALPHA1-6 : angle 1.96694 ( 18) link_BETA1-4 : bond 0.01331 ( 23) link_BETA1-4 : angle 3.58678 ( 69) link_NAG-ASN : bond 0.00485 ( 34) link_NAG-ASN : angle 2.64198 ( 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 : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9413 (ttm) cc_final: 0.9210 (ttt) REVERT: C 213 LYS cc_start: 0.9592 (mmtt) cc_final: 0.9261 (mmtm) REVERT: E 151 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: E 417 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8244 (mp10) REVERT: F 530 MET cc_start: 0.8288 (mtp) cc_final: 0.7875 (mtp) REVERT: G 213 LYS cc_start: 0.9435 (mmtt) cc_final: 0.9043 (mmtm) REVERT: G 218 LYS cc_start: 0.9243 (pttt) cc_final: 0.8917 (tttp) REVERT: J 614 TRP cc_start: 0.6172 (OUTLIER) cc_final: 0.5704 (m-10) outliers start: 23 outliers final: 5 residues processed: 82 average time/residue: 0.1779 time to fit residues: 23.2166 Evaluate side-chains 65 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 158 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 255 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 404 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.040243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.030080 restraints weight = 252935.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.030872 restraints weight = 145349.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.031371 restraints weight = 105778.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.031632 restraints weight = 87457.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.031860 restraints weight = 78908.020| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25704 Z= 0.181 Angle : 0.737 10.977 35114 Z= 0.366 Chirality : 0.048 0.246 4119 Planarity : 0.005 0.053 4376 Dihedral : 9.289 59.259 4772 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.65 % Favored : 94.02 % Rotamer: Outliers : 1.14 % Allowed : 6.70 % Favored : 92.15 % 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 aren not related in a simple way. whole: -0.41 (0.16), residues: 3078 helix: 0.80 (0.26), residues: 465 sheet: -0.31 (0.16), residues: 1017 loop : -0.47 (0.17), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 617 TYR 0.021 0.002 TYR A 484 PHE 0.019 0.002 PHE A 376 TRP 0.021 0.002 TRP I 112 HIS 0.009 0.002 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00411 (25587) covalent geometry : angle 0.70868 (34811) SS BOND : bond 0.00303 ( 48) SS BOND : angle 0.97192 ( 96) hydrogen bonds : bond 0.04206 ( 934) hydrogen bonds : angle 6.16735 ( 2574) link_ALPHA1-3 : bond 0.00363 ( 6) link_ALPHA1-3 : angle 3.93323 ( 18) link_ALPHA1-6 : bond 0.01023 ( 6) link_ALPHA1-6 : angle 2.08144 ( 18) link_BETA1-4 : bond 0.01118 ( 23) link_BETA1-4 : angle 3.02504 ( 69) link_NAG-ASN : bond 0.00417 ( 34) link_NAG-ASN : angle 2.20985 ( 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 91 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 1.069 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: 0.9588 (mmtt) cc_final: 0.9238 (mmtm) REVERT: E 135 THR cc_start: 0.4077 (OUTLIER) cc_final: 0.3803 (p) REVERT: E 417 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: F 530 MET cc_start: 0.8579 (mtp) cc_final: 0.8140 (mtp) REVERT: G 213 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9020 (mppt) REVERT: G 218 LYS cc_start: 0.9199 (pttt) cc_final: 0.8886 (tttp) REVERT: H 4 MET cc_start: 0.8442 (tpp) cc_final: 0.8189 (tpp) REVERT: I 135 THR cc_start: 0.3772 (OUTLIER) cc_final: 0.3485 (p) REVERT: J 540 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7776 (tp40) REVERT: K 218 LYS cc_start: 0.9203 (pttt) cc_final: 0.8802 (tptt) outliers start: 31 outliers final: 10 residues processed: 87 average time/residue: 0.1841 time to fit residues: 26.2435 Evaluate side-chains 70 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 13 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 204 optimal weight: 8.9990 chunk 109 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 194 optimal weight: 30.0000 chunk 231 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 126 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN G 52 ASN I 315 GLN I 350 GLN ** J 540 GLN ** 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 = 0.3474 r_free = 0.3474 target = 0.039057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.028835 restraints weight = 250597.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.029573 restraints weight = 147205.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.030015 restraints weight = 108631.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030285 restraints weight = 91165.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.030430 restraints weight = 82125.080| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 25704 Z= 0.374 Angle : 0.910 11.465 35114 Z= 0.444 Chirality : 0.052 0.246 4119 Planarity : 0.005 0.059 4376 Dihedral : 9.425 60.318 4772 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 1.36 % Allowed : 8.36 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 aren not related in a simple way. whole: -0.84 (0.15), residues: 3078 helix: 0.33 (0.24), residues: 483 sheet: -0.50 (0.16), residues: 996 loop : -0.80 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 44 TYR 0.022 0.003 TYR I 61 PHE 0.029 0.003 PHE E 376 TRP 0.023 0.003 TRP A 112 HIS 0.010 0.003 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00867 (25587) covalent geometry : angle 0.88246 (34811) SS BOND : bond 0.00468 ( 48) SS BOND : angle 1.23790 ( 96) hydrogen bonds : bond 0.05001 ( 934) hydrogen bonds : angle 6.56217 ( 2574) link_ALPHA1-3 : bond 0.00213 ( 6) link_ALPHA1-3 : angle 4.26631 ( 18) link_ALPHA1-6 : bond 0.00717 ( 6) link_ALPHA1-6 : angle 2.97740 ( 18) link_BETA1-4 : bond 0.01165 ( 23) link_BETA1-4 : angle 3.13566 ( 69) link_NAG-ASN : bond 0.00791 ( 34) link_NAG-ASN : angle 2.58079 ( 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 92 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 1.077 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: 0.9566 (mmtt) cc_final: 0.9225 (mppt) REVERT: E 135 THR cc_start: 0.3599 (OUTLIER) cc_final: 0.3323 (p) REVERT: E 417 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: F 530 MET cc_start: 0.8538 (mtp) cc_final: 0.7950 (mtp) REVERT: G 213 LYS cc_start: 0.9457 (mmtt) cc_final: 0.9061 (mmtm) REVERT: G 218 LYS cc_start: 0.9252 (pttt) cc_final: 0.8892 (tttp) REVERT: I 467 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7825 (p) REVERT: J 540 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7806 (tp40) outliers start: 37 outliers final: 16 residues processed: 84 average time/residue: 0.1798 time to fit residues: 25.0990 Evaluate side-chains 75 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 326 ILE 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 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 141 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 289 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN 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 = 0.039823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.029721 restraints weight = 252309.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.030493 restraints weight = 144838.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.030985 restraints weight = 105648.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.031288 restraints weight = 87448.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031403 restraints weight = 78132.698| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 25704 Z= 0.159 Angle : 0.683 10.572 35114 Z= 0.338 Chirality : 0.046 0.241 4119 Planarity : 0.004 0.056 4376 Dihedral : 8.546 57.272 4772 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.78 % Favored : 93.96 % Rotamer: Outliers : 0.77 % Allowed : 9.06 % Favored : 90.17 % 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 aren not related in a simple way. whole: -0.55 (0.16), residues: 3078 helix: 1.07 (0.26), residues: 465 sheet: -0.49 (0.16), residues: 1023 loop : -0.63 (0.17), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 617 TYR 0.021 0.001 TYR I 61 PHE 0.019 0.002 PHE E 376 TRP 0.021 0.002 TRP I 112 HIS 0.008 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00350 (25587) covalent geometry : angle 0.65582 (34811) SS BOND : bond 0.00256 ( 48) SS BOND : angle 0.85591 ( 96) hydrogen bonds : bond 0.03937 ( 934) hydrogen bonds : angle 5.98271 ( 2574) link_ALPHA1-3 : bond 0.00457 ( 6) link_ALPHA1-3 : angle 4.39994 ( 18) link_ALPHA1-6 : bond 0.01054 ( 6) link_ALPHA1-6 : angle 1.56332 ( 18) link_BETA1-4 : bond 0.00959 ( 23) link_BETA1-4 : angle 2.80293 ( 69) link_NAG-ASN : bond 0.00316 ( 34) link_NAG-ASN : angle 2.03087 ( 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 78 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9590 (mmtt) cc_final: 0.9222 (mmtm) REVERT: E 135 THR cc_start: 0.3865 (OUTLIER) cc_final: 0.3643 (p) REVERT: E 417 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: F 530 MET cc_start: 0.8603 (mtp) cc_final: 0.8128 (mtp) REVERT: G 34 MET cc_start: 0.9219 (mmm) cc_final: 0.8948 (mmm) REVERT: G 213 LYS cc_start: 0.9477 (mmtt) cc_final: 0.9001 (mppt) REVERT: K 218 LYS cc_start: 0.9220 (pttt) cc_final: 0.8788 (tptt) outliers start: 21 outliers final: 11 residues processed: 76 average time/residue: 0.1744 time to fit residues: 22.3002 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 : 1.012 ------------------------------------------------------------------------------- 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 D residue 206 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 417 GLN 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 K residue 162 VAL Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 155 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 70 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN I 300 ASN I 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.039461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.029326 restraints weight = 254540.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.030088 restraints weight = 147697.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.030583 restraints weight = 107615.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.030854 restraints weight = 89349.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.031001 restraints weight = 80292.279| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3159 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= 0.226 Angle : 0.721 10.628 35114 Z= 0.354 Chirality : 0.046 0.225 4119 Planarity : 0.004 0.056 4376 Dihedral : 8.599 58.994 4772 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.43 % Favored : 93.31 % Rotamer: Outliers : 1.51 % Allowed : 9.21 % Favored : 89.28 % 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 aren not related in a simple way. whole: -0.61 (0.16), residues: 3078 helix: 1.06 (0.26), residues: 468 sheet: -0.56 (0.16), residues: 1029 loop : -0.65 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 216 TYR 0.020 0.002 TYR I 61 PHE 0.021 0.002 PHE E 376 TRP 0.021 0.002 TRP I 112 HIS 0.007 0.002 HIS I 330 Details of bonding type rmsd covalent geometry : bond 0.00514 (25587) covalent geometry : angle 0.69348 (34811) SS BOND : bond 0.00331 ( 48) SS BOND : angle 0.89888 ( 96) hydrogen bonds : bond 0.04016 ( 934) hydrogen bonds : angle 5.98299 ( 2574) link_ALPHA1-3 : bond 0.00287 ( 6) link_ALPHA1-3 : angle 4.30352 ( 18) link_ALPHA1-6 : bond 0.00609 ( 6) link_ALPHA1-6 : angle 1.99388 ( 18) link_BETA1-4 : bond 0.00951 ( 23) link_BETA1-4 : angle 2.84914 ( 69) link_NAG-ASN : bond 0.00495 ( 34) link_NAG-ASN : angle 2.15421 ( 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 96 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 55 time to evaluate : 1.199 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: 0.9567 (mmtt) cc_final: 0.9209 (mppt) REVERT: E 135 THR cc_start: 0.3835 (OUTLIER) cc_final: 0.3595 (p) REVERT: E 417 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: F 530 MET cc_start: 0.8512 (mtp) cc_final: 0.8187 (mtp) REVERT: G 34 MET cc_start: 0.9195 (mmm) cc_final: 0.8818 (mmm) REVERT: G 213 LYS cc_start: 0.9454 (mmtt) cc_final: 0.8982 (mppt) REVERT: I 213 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8820 (tp) REVERT: I 467 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7854 (p) REVERT: K 218 LYS cc_start: 0.9217 (pttt) cc_final: 0.8787 (tptt) outliers start: 41 outliers final: 22 residues processed: 90 average time/residue: 0.1693 time to fit residues: 25.7478 Evaluate side-chains 80 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 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 C residue 194 VAL Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 417 GLN 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 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR 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 4 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 248 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.039788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.029742 restraints weight = 252613.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.030528 restraints weight = 144364.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.031022 restraints weight = 104865.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.031307 restraints weight = 86692.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.031482 restraints weight = 77753.606| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25704 Z= 0.154 Angle : 0.649 10.108 35114 Z= 0.321 Chirality : 0.045 0.216 4119 Planarity : 0.004 0.053 4376 Dihedral : 8.139 59.637 4772 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.78 % Favored : 93.96 % Rotamer: Outliers : 1.14 % Allowed : 9.80 % Favored : 89.06 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 3078 helix: 1.28 (0.26), residues: 468 sheet: -0.49 (0.16), residues: 1029 loop : -0.52 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 216 TYR 0.020 0.001 TYR I 61 PHE 0.018 0.001 PHE E 376 TRP 0.018 0.002 TRP I 427 HIS 0.007 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00343 (25587) covalent geometry : angle 0.62109 (34811) SS BOND : bond 0.00262 ( 48) SS BOND : angle 0.76478 ( 96) hydrogen bonds : bond 0.03594 ( 934) hydrogen bonds : angle 5.71918 ( 2574) link_ALPHA1-3 : bond 0.00556 ( 6) link_ALPHA1-3 : angle 4.37469 ( 18) link_ALPHA1-6 : bond 0.00530 ( 6) link_ALPHA1-6 : angle 1.80820 ( 18) link_BETA1-4 : bond 0.00929 ( 23) link_BETA1-4 : angle 2.75893 ( 69) link_NAG-ASN : bond 0.00307 ( 34) link_NAG-ASN : angle 1.91150 ( 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 86 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 1.070 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: 0.7982 (OUTLIER) cc_final: 0.6700 (tm-30) REVERT: C 213 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9207 (mmtm) REVERT: E 417 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: F 530 MET cc_start: 0.8590 (mtp) cc_final: 0.8148 (mtp) REVERT: G 218 LYS cc_start: 0.9264 (pttt) cc_final: 0.8877 (tttp) REVERT: J 614 TRP cc_start: 0.6415 (OUTLIER) cc_final: 0.5867 (m-10) REVERT: K 218 LYS cc_start: 0.9233 (pttt) cc_final: 0.8783 (tptt) outliers start: 31 outliers final: 16 residues processed: 83 average time/residue: 0.1662 time to fit residues: 23.0710 Evaluate side-chains 72 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 77 THR 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 149 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 CYS 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 J residue 614 TRP Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain L residue 4 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 236 optimal weight: 0.7980 chunk 303 optimal weight: 40.0000 chunk 171 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 146 optimal weight: 0.1980 chunk 187 optimal weight: 3.9990 chunk 203 optimal weight: 40.0000 chunk 86 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 243 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.040015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.029987 restraints weight = 251441.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.030797 restraints weight = 140852.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.031313 restraints weight = 100633.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.031634 restraints weight = 82407.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.031766 restraints weight = 73040.839| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 25704 Z= 0.110 Angle : 0.617 10.249 35114 Z= 0.305 Chirality : 0.044 0.206 4119 Planarity : 0.004 0.051 4376 Dihedral : 7.738 59.233 4772 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 0.85 % Allowed : 10.35 % Favored : 88.80 % 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 aren not related in a simple way. whole: -0.36 (0.16), residues: 3078 helix: 1.38 (0.26), residues: 468 sheet: -0.48 (0.16), residues: 1062 loop : -0.47 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 216 TYR 0.020 0.001 TYR L 92 PHE 0.016 0.001 PHE A 376 TRP 0.015 0.001 TRP G 106 HIS 0.006 0.001 HIS I 374 Details of bonding type rmsd covalent geometry : bond 0.00235 (25587) covalent geometry : angle 0.59003 (34811) SS BOND : bond 0.00227 ( 48) SS BOND : angle 0.66770 ( 96) hydrogen bonds : bond 0.03259 ( 934) hydrogen bonds : angle 5.46907 ( 2574) link_ALPHA1-3 : bond 0.00751 ( 6) link_ALPHA1-3 : angle 4.25485 ( 18) link_ALPHA1-6 : bond 0.00586 ( 6) link_ALPHA1-6 : angle 1.69848 ( 18) link_BETA1-4 : bond 0.00932 ( 23) link_BETA1-4 : angle 2.71497 ( 69) link_NAG-ASN : bond 0.00231 ( 34) link_NAG-ASN : angle 1.78780 ( 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 83 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 1.067 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: 0.7921 (OUTLIER) cc_final: 0.6679 (tm-30) REVERT: C 213 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9212 (mmtm) REVERT: C 218 LYS cc_start: 0.9215 (pttt) cc_final: 0.8747 (tptt) REVERT: E 417 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: F 530 MET cc_start: 0.8584 (mtp) cc_final: 0.8168 (mtp) REVERT: G 213 LYS cc_start: 0.9471 (mmtt) cc_final: 0.9013 (mmtm) REVERT: G 218 LYS cc_start: 0.9250 (pttt) cc_final: 0.8813 (tptt) REVERT: I 213 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8851 (tp) REVERT: J 614 TRP cc_start: 0.6215 (OUTLIER) cc_final: 0.5701 (m-10) REVERT: K 34 MET cc_start: 0.9083 (mmm) cc_final: 0.8787 (mmm) REVERT: K 218 LYS cc_start: 0.9237 (pttt) cc_final: 0.8805 (tptt) outliers start: 23 outliers final: 15 residues processed: 81 average time/residue: 0.1674 time to fit residues: 22.4955 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 : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE 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 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 242 optimal weight: 3.9990 chunk 36 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 200 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN H 96 ASN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 651 ASN L 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.039051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.029042 restraints weight = 252712.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.029784 restraints weight = 147503.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030243 restraints weight = 107819.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.030511 restraints weight = 89810.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.030653 restraints weight = 80892.651| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 25704 Z= 0.325 Angle : 0.805 9.774 35114 Z= 0.393 Chirality : 0.049 0.229 4119 Planarity : 0.005 0.056 4376 Dihedral : 8.520 59.847 4772 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.99 % Favored : 92.76 % Rotamer: Outliers : 1.07 % Allowed : 10.13 % Favored : 88.80 % 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 aren not related in a simple way. whole: -0.64 (0.16), residues: 3078 helix: 0.92 (0.25), residues: 468 sheet: -0.61 (0.16), residues: 1029 loop : -0.61 (0.17), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 44 TYR 0.022 0.002 TYR E 61 PHE 0.024 0.003 PHE E 376 TRP 0.022 0.002 TRP I 479 HIS 0.006 0.002 HIS K 212 Details of bonding type rmsd covalent geometry : bond 0.00741 (25587) covalent geometry : angle 0.77598 (34811) SS BOND : bond 0.00453 ( 48) SS BOND : angle 1.07455 ( 96) hydrogen bonds : bond 0.04339 ( 934) hydrogen bonds : angle 6.01793 ( 2574) link_ALPHA1-3 : bond 0.00433 ( 6) link_ALPHA1-3 : angle 3.81090 ( 18) link_ALPHA1-6 : bond 0.00748 ( 6) link_ALPHA1-6 : angle 2.90677 ( 18) link_BETA1-4 : bond 0.01067 ( 23) link_BETA1-4 : angle 3.10582 ( 69) link_NAG-ASN : bond 0.00776 ( 34) link_NAG-ASN : angle 2.43933 ( 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 83 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 1.160 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: 0.9558 (mmtt) cc_final: 0.9203 (mmtm) REVERT: E 417 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8327 (mp10) REVERT: F 530 MET cc_start: 0.8463 (mtp) cc_final: 0.7988 (mtp) REVERT: G 218 LYS cc_start: 0.9236 (pttt) cc_final: 0.8750 (tptt) REVERT: I 213 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8976 (tp) outliers start: 29 outliers final: 23 residues processed: 79 average time/residue: 0.1573 time to fit residues: 21.3213 Evaluate side-chains 78 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE 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 C residue 194 VAL Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 257 THR 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 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 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP 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 4 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 75 optimal weight: 20.0000 chunk 279 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 250 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 238 optimal weight: 0.9980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN 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 = 0.039808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.029816 restraints weight = 253420.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.030596 restraints weight = 144797.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.031094 restraints weight = 105276.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.031377 restraints weight = 87256.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.031536 restraints weight = 78207.181| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3618 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= 0.132 Angle : 0.639 9.501 35114 Z= 0.315 Chirality : 0.044 0.211 4119 Planarity : 0.004 0.045 4376 Dihedral : 7.859 58.144 4772 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 0.77 % Allowed : 10.57 % Favored : 88.66 % 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 aren not related in a simple way. whole: -0.43 (0.16), residues: 3078 helix: 1.30 (0.26), residues: 468 sheet: -0.48 (0.16), residues: 1071 loop : -0.55 (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 G 33 PHE 0.017 0.001 PHE A 376 TRP 0.019 0.002 TRP E 112 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (25587) covalent geometry : angle 0.61114 (34811) SS BOND : bond 0.00308 ( 48) SS BOND : angle 0.85231 ( 96) hydrogen bonds : bond 0.03469 ( 934) hydrogen bonds : angle 5.55190 ( 2574) link_ALPHA1-3 : bond 0.00783 ( 6) link_ALPHA1-3 : angle 4.12050 ( 18) link_ALPHA1-6 : bond 0.00384 ( 6) link_ALPHA1-6 : angle 1.95010 ( 18) link_BETA1-4 : bond 0.00866 ( 23) link_BETA1-4 : angle 2.78318 ( 69) link_NAG-ASN : bond 0.00249 ( 34) link_NAG-ASN : angle 1.82162 ( 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 78 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.691 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: 0.8007 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: C 213 LYS cc_start: 0.9567 (mmtt) cc_final: 0.9201 (mmtm) REVERT: E 417 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8240 (mp10) REVERT: F 530 MET cc_start: 0.8534 (mtp) cc_final: 0.8047 (mtp) REVERT: G 218 LYS cc_start: 0.9271 (pttt) cc_final: 0.8798 (tptt) REVERT: I 213 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8994 (tp) REVERT: K 34 MET cc_start: 0.9030 (mmm) cc_final: 0.8776 (mmm) REVERT: K 218 LYS cc_start: 0.9251 (pttt) cc_final: 0.8799 (tptt) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.1594 time to fit residues: 20.1061 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 : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 326 ILE 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 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 178 ASP 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 204 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 135 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.039223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.029271 restraints weight = 250763.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.030014 restraints weight = 145560.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.030472 restraints weight = 106569.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.030750 restraints weight = 88831.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.030917 restraints weight = 79807.591| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25704 Z= 0.257 Angle : 0.724 9.694 35114 Z= 0.355 Chirality : 0.046 0.229 4119 Planarity : 0.004 0.050 4376 Dihedral : 8.194 58.089 4772 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.86 % Favored : 92.88 % Rotamer: Outliers : 0.92 % Allowed : 10.46 % Favored : 88.62 % 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 aren not related in a simple way. whole: -0.56 (0.16), residues: 3078 helix: 1.14 (0.26), residues: 468 sheet: -0.57 (0.16), residues: 1089 loop : -0.59 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 617 TYR 0.019 0.002 TYR E 61 PHE 0.022 0.002 PHE E 376 TRP 0.019 0.002 TRP A 112 HIS 0.006 0.002 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00587 (25587) covalent geometry : angle 0.69632 (34811) SS BOND : bond 0.00345 ( 48) SS BOND : angle 0.93615 ( 96) hydrogen bonds : bond 0.03943 ( 934) hydrogen bonds : angle 5.75330 ( 2574) link_ALPHA1-3 : bond 0.00570 ( 6) link_ALPHA1-3 : angle 3.78906 ( 18) link_ALPHA1-6 : bond 0.00497 ( 6) link_ALPHA1-6 : angle 2.48071 ( 18) link_BETA1-4 : bond 0.00953 ( 23) link_BETA1-4 : angle 2.94210 ( 69) link_NAG-ASN : bond 0.00610 ( 34) link_NAG-ASN : angle 2.18881 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4197.32 seconds wall clock time: 73 minutes 45.45 seconds (4425.45 seconds total)