Starting phenix.real_space_refine on Sat Jun 21 19:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dow_27624/06_2025/8dow_27624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dow_27624/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dow_27624/06_2025/8dow_27624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dow_27624/06_2025/8dow_27624.map" model { file = "/net/cci-nas-00/data/ceres_data/8dow_27624/06_2025/8dow_27624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dow_27624/06_2025/8dow_27624.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 14.61, per 1000 atoms: 0.58 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: 7.36 Conformation dependent library (CDL) restraints added in 3.3 seconds 6156 Ramachandran restraints generated. 3078 Oldfield, 0 Emsley, 3078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 57 sheets defined 20.4% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.22 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: 11.08 Time building geometry restraints manager: 8.26 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: 2.030 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: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 60.080 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.790 ------------------------------------------------------------------------------- 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 : 0.14 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.268 0.029 TRP F 623 HIS 0.036 0.006 HIS C 111 PHE 0.114 0.018 PHE K 27 TYR 0.152 0.022 TYR E 400 ARG 0.011 0.002 ARG G 56 Details of bonding type rmsd link_NAG-ASN : bond 0.01110 ( 34) link_NAG-ASN : angle 4.47225 ( 102) 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_ALPHA1-3 : bond 0.02526 ( 6) link_ALPHA1-3 : angle 7.78590 ( 18) hydrogen bonds : bond 0.16093 ( 934) hydrogen bonds : angle 9.21406 ( 2574) SS BOND : bond 0.00610 ( 48) SS BOND : angle 2.41733 ( 96) covalent geometry : bond 0.01371 (25587) covalent geometry : angle 1.91486 (34811) *********************** 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 : 2.673 Fit side-chains 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: C 218 LYS cc_start: 0.9113 (pttt) cc_final: 0.8667 (tttp) REVERT: E 66 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6638 (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: 0.8240 (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: 4 residues processed: 116 average time/residue: 0.4698 time to fit residues: 81.1057 Evaluate side-chains 63 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP 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 258 optimal weight: 6.9990 chunk 231 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 50.0000 chunk 156 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 92 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 277 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.040301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.030281 restraints weight = 245468.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.031047 restraints weight = 140764.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.031523 restraints weight = 102154.325| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1754 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= 0.207 Angle : 0.855 12.815 35114 Z= 0.430 Chirality : 0.050 0.300 4119 Planarity : 0.005 0.052 4376 Dihedral : 11.351 76.013 4783 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.23 % Favored : 94.35 % Rotamer: Outliers : 0.88 % Allowed : 6.00 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3078 helix: 0.02 (0.24), residues: 471 sheet: -0.31 (0.16), residues: 954 loop : -0.54 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP I 112 HIS 0.009 0.002 HIS A 374 PHE 0.019 0.002 PHE A 376 TYR 0.018 0.002 TYR I 61 ARG 0.005 0.001 ARG D 28 Details of bonding type rmsd link_NAG-ASN : bond 0.00524 ( 34) link_NAG-ASN : angle 2.72647 ( 102) link_ALPHA1-6 : bond 0.00952 ( 6) link_ALPHA1-6 : angle 2.34460 ( 18) link_BETA1-4 : bond 0.01383 ( 23) link_BETA1-4 : angle 3.53020 ( 69) link_ALPHA1-3 : bond 0.00876 ( 6) link_ALPHA1-3 : angle 4.43967 ( 18) hydrogen bonds : bond 0.05235 ( 934) hydrogen bonds : angle 7.03028 ( 2574) SS BOND : bond 0.00273 ( 48) SS BOND : angle 1.04908 ( 96) covalent geometry : bond 0.00464 (25587) covalent geometry : angle 0.82122 (34811) *********************** 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 85 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 2.944 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: 0.9597 (mmtt) cc_final: 0.9273 (mmtm) REVERT: E 151 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7822 (mm-30) REVERT: E 417 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: F 530 MET cc_start: 0.8435 (mtp) cc_final: 0.7962 (mtp) REVERT: G 213 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9058 (mmtm) REVERT: G 218 LYS cc_start: 0.9162 (pttt) cc_final: 0.8948 (ttmm) outliers start: 24 outliers final: 6 residues processed: 83 average time/residue: 0.3991 time to fit residues: 54.1049 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 : 2.979 ------------------------------------------------------------------------------- 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 F residue 540 GLN Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain J residue 569 THR 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 47 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 275 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 304 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 350 GLN ** 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 = 0.3502 r_free = 0.3502 target = 0.039700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.029541 restraints weight = 253080.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030304 restraints weight = 146939.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.030780 restraints weight = 107760.201| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25704 Z= 0.251 Angle : 0.802 11.165 35114 Z= 0.397 Chirality : 0.049 0.239 4119 Planarity : 0.005 0.057 4376 Dihedral : 9.658 67.298 4775 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.43 % Favored : 93.24 % Rotamer: Outliers : 1.40 % Allowed : 7.26 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 3078 helix: 0.44 (0.25), residues: 483 sheet: -0.44 (0.16), residues: 996 loop : -0.70 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 112 HIS 0.009 0.002 HIS I 287 PHE 0.023 0.002 PHE E 376 TYR 0.024 0.002 TYR A 484 ARG 0.005 0.001 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00571 ( 34) link_NAG-ASN : angle 2.33963 ( 102) link_ALPHA1-6 : bond 0.00870 ( 6) link_ALPHA1-6 : angle 2.26485 ( 18) link_BETA1-4 : bond 0.01131 ( 23) link_BETA1-4 : angle 2.99516 ( 69) link_ALPHA1-3 : bond 0.00234 ( 6) link_ALPHA1-3 : angle 4.05982 ( 18) hydrogen bonds : bond 0.04553 ( 934) hydrogen bonds : angle 6.41557 ( 2574) SS BOND : bond 0.00427 ( 48) SS BOND : angle 1.08890 ( 96) covalent geometry : bond 0.00574 (25587) covalent geometry : angle 0.77462 (34811) *********************** 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 98 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 3.446 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: 0.9604 (mmtt) cc_final: 0.9247 (mppt) REVERT: E 135 THR cc_start: 0.3745 (OUTLIER) cc_final: 0.3452 (p) REVERT: E 417 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8264 (mp10) REVERT: F 530 MET cc_start: 0.8521 (mtp) cc_final: 0.7901 (mtp) REVERT: G 213 LYS cc_start: 0.9491 (mmtt) cc_final: 0.9071 (mmtm) REVERT: G 218 LYS cc_start: 0.9234 (pttt) cc_final: 0.8880 (tttp) REVERT: J 540 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7844 (tp40) REVERT: J 614 TRP cc_start: 0.6433 (OUTLIER) cc_final: 0.5743 (m-10) REVERT: K 218 LYS cc_start: 0.9247 (pttt) cc_final: 0.8827 (tptt) outliers start: 38 outliers final: 15 residues processed: 92 average time/residue: 0.3861 time to fit residues: 59.4403 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 : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain 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 F residue 540 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain I residue 149 VAL 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 J residue 614 TRP Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 195 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 292 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 265 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 404 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN I 315 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.039856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.029673 restraints weight = 253722.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.031062 restraints weight = 161172.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.031315 restraints weight = 93176.728| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25704 Z= 0.185 Angle : 0.710 10.312 35114 Z= 0.350 Chirality : 0.047 0.260 4119 Planarity : 0.004 0.058 4376 Dihedral : 8.709 70.727 4775 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.36 % Favored : 94.35 % Rotamer: Outliers : 1.18 % Allowed : 8.43 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 3078 helix: 0.98 (0.26), residues: 465 sheet: -0.45 (0.16), residues: 984 loop : -0.57 (0.17), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.010 0.002 HIS E 105 PHE 0.019 0.002 PHE E 376 TYR 0.019 0.002 TYR A 61 ARG 0.007 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00367 ( 34) link_NAG-ASN : angle 2.08837 ( 102) link_ALPHA1-6 : bond 0.01143 ( 6) link_ALPHA1-6 : angle 1.94734 ( 18) link_BETA1-4 : bond 0.00982 ( 23) link_BETA1-4 : angle 2.86606 ( 69) link_ALPHA1-3 : bond 0.00338 ( 6) link_ALPHA1-3 : angle 4.39745 ( 18) hydrogen bonds : bond 0.04002 ( 934) hydrogen bonds : angle 6.06028 ( 2574) SS BOND : bond 0.00359 ( 48) SS BOND : angle 0.87638 ( 96) covalent geometry : bond 0.00416 (25587) covalent geometry : angle 0.68188 (34811) *********************** 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 88 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 3.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9563 (mmtt) cc_final: 0.9191 (mppt) REVERT: E 135 THR cc_start: 0.3858 (OUTLIER) cc_final: 0.3583 (p) REVERT: E 417 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: F 530 MET cc_start: 0.8491 (mtp) cc_final: 0.7962 (mtp) REVERT: G 34 MET cc_start: 0.9190 (mmm) cc_final: 0.8837 (mmm) REVERT: G 213 LYS cc_start: 0.9439 (mmtt) cc_final: 0.8958 (mppt) REVERT: G 218 LYS cc_start: 0.9189 (pttt) cc_final: 0.8744 (tttp) REVERT: I 467 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7895 (p) REVERT: J 614 TRP cc_start: 0.6420 (OUTLIER) cc_final: 0.5731 (m-10) REVERT: K 218 LYS cc_start: 0.9165 (pttt) cc_final: 0.8710 (tptt) outliers start: 32 outliers final: 13 residues processed: 84 average time/residue: 0.3883 time to fit residues: 55.5297 Evaluate side-chains 72 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain 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 417 GLN Chi-restraints excluded: chain F residue 540 GLN 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 467 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 150 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 275 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.0050 chunk 126 optimal weight: 4.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- 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 ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 ASN I 300 ASN I 404 ASN ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.039723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.029610 restraints weight = 253280.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.030381 restraints weight = 146422.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.030850 restraints weight = 106743.663| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25704 Z= 0.191 Angle : 0.693 10.409 35114 Z= 0.341 Chirality : 0.046 0.226 4119 Planarity : 0.004 0.058 4376 Dihedral : 8.547 74.766 4775 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.53 % Rotamer: Outliers : 1.33 % Allowed : 9.06 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 3078 helix: 1.02 (0.26), residues: 468 sheet: -0.51 (0.15), residues: 1065 loop : -0.58 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 112 HIS 0.008 0.002 HIS E 105 PHE 0.020 0.002 PHE E 376 TYR 0.019 0.002 TYR I 61 ARG 0.004 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 34) link_NAG-ASN : angle 2.07903 ( 102) link_ALPHA1-6 : bond 0.00904 ( 6) link_ALPHA1-6 : angle 1.77382 ( 18) link_BETA1-4 : bond 0.00988 ( 23) link_BETA1-4 : angle 2.79528 ( 69) link_ALPHA1-3 : bond 0.00350 ( 6) link_ALPHA1-3 : angle 4.23480 ( 18) hydrogen bonds : bond 0.03882 ( 934) hydrogen bonds : angle 5.90232 ( 2574) SS BOND : bond 0.00286 ( 48) SS BOND : angle 0.86329 ( 96) covalent geometry : bond 0.00431 (25587) covalent geometry : angle 0.66596 (34811) *********************** 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 94 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 58 time to evaluate : 3.180 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: symmetry clash REVERT: C 213 LYS cc_start: 0.9588 (mmtt) cc_final: 0.9212 (mppt) REVERT: E 135 THR cc_start: 0.3825 (OUTLIER) cc_final: 0.3603 (p) REVERT: E 417 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8262 (mp10) REVERT: F 530 MET cc_start: 0.8539 (mtp) cc_final: 0.8012 (mtp) REVERT: G 34 MET cc_start: 0.9166 (mmm) cc_final: 0.8839 (mmm) REVERT: G 213 LYS cc_start: 0.9481 (mmtt) cc_final: 0.9003 (mppt) REVERT: G 218 LYS cc_start: 0.9242 (pttt) cc_final: 0.8824 (tttp) REVERT: I 467 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7863 (p) REVERT: J 540 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7846 (tp40) REVERT: K 218 LYS cc_start: 0.9210 (pttt) cc_final: 0.8769 (tptt) outliers start: 36 outliers final: 20 residues processed: 90 average time/residue: 0.3597 time to fit residues: 54.8997 Evaluate side-chains 80 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain 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 540 GLN Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 201 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 27 optimal weight: 0.0020 chunk 247 optimal weight: 3.9990 overall best weight: 5.7996 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.039282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.029181 restraints weight = 252960.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.029949 restraints weight = 147598.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.030410 restraints weight = 107756.031| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25704 Z= 0.259 Angle : 0.749 10.730 35114 Z= 0.368 Chirality : 0.047 0.230 4119 Planarity : 0.005 0.054 4376 Dihedral : 8.770 81.691 4775 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.66 % Favored : 93.08 % Rotamer: Outliers : 1.69 % Allowed : 9.43 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 3078 helix: 0.92 (0.25), residues: 468 sheet: -0.59 (0.16), residues: 1047 loop : -0.63 (0.17), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 112 HIS 0.007 0.002 HIS I 330 PHE 0.023 0.002 PHE E 376 TYR 0.021 0.002 TYR I 61 ARG 0.005 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 34) link_NAG-ASN : angle 2.23877 ( 102) link_ALPHA1-6 : bond 0.00512 ( 6) link_ALPHA1-6 : angle 2.21918 ( 18) link_BETA1-4 : bond 0.01015 ( 23) link_BETA1-4 : angle 2.90709 ( 69) link_ALPHA1-3 : bond 0.00312 ( 6) link_ALPHA1-3 : angle 4.19080 ( 18) hydrogen bonds : bond 0.04182 ( 934) hydrogen bonds : angle 6.04900 ( 2574) SS BOND : bond 0.00356 ( 48) SS BOND : angle 0.96915 ( 96) covalent geometry : bond 0.00591 (25587) covalent geometry : angle 0.72126 (34811) *********************** 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 100 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 54 time to evaluate : 2.721 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: 0.9568 (mmtt) cc_final: 0.9204 (mppt) REVERT: E 135 THR cc_start: 0.3919 (OUTLIER) cc_final: 0.3680 (p) REVERT: E 417 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8283 (mp10) REVERT: F 530 MET cc_start: 0.8531 (mtp) cc_final: 0.8041 (mtp) REVERT: G 218 LYS cc_start: 0.9239 (pttt) cc_final: 0.8824 (tttp) REVERT: I 213 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8917 (tp) REVERT: I 467 THR cc_start: 0.8279 (OUTLIER) cc_final: 0.7816 (p) REVERT: J 540 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7953 (tp40) outliers start: 46 outliers final: 25 residues processed: 96 average time/residue: 0.3372 time to fit residues: 55.9583 Evaluate side-chains 84 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 100 MET 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 135 THR 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 257 THR Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain I residue 37 THR 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 I residue 178 ASP 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 518 VAL Chi-restraints excluded: chain J residue 540 GLN Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain K residue 106 TRP Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 276 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 159 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN ** I 67 ASN ** 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 = 0.3492 r_free = 0.3492 target = 0.039423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.029371 restraints weight = 252949.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.030136 restraints weight = 145891.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.030616 restraints weight = 106636.029| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25704 Z= 0.210 Angle : 0.696 9.733 35114 Z= 0.343 Chirality : 0.046 0.227 4119 Planarity : 0.004 0.053 4376 Dihedral : 8.390 59.545 4772 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.66 % Favored : 93.08 % Rotamer: Outliers : 1.36 % Allowed : 10.46 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.16), residues: 3078 helix: 1.04 (0.26), residues: 468 sheet: -0.58 (0.16), residues: 1047 loop : -0.65 (0.17), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 112 HIS 0.007 0.002 HIS E 374 PHE 0.021 0.002 PHE E 376 TYR 0.019 0.002 TYR E 61 ARG 0.004 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 34) link_NAG-ASN : angle 2.07843 ( 102) link_ALPHA1-6 : bond 0.00444 ( 6) link_ALPHA1-6 : angle 2.17662 ( 18) link_BETA1-4 : bond 0.00974 ( 23) link_BETA1-4 : angle 2.85259 ( 69) link_ALPHA1-3 : bond 0.00483 ( 6) link_ALPHA1-3 : angle 4.24674 ( 18) hydrogen bonds : bond 0.03907 ( 934) hydrogen bonds : angle 5.90081 ( 2574) SS BOND : bond 0.00311 ( 48) SS BOND : angle 0.87474 ( 96) covalent geometry : bond 0.00475 (25587) covalent geometry : angle 0.66773 (34811) *********************** 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 91 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 2.760 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: 0.9570 (mmtt) cc_final: 0.9208 (mmtm) REVERT: E 417 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8320 (mp10) REVERT: F 530 MET cc_start: 0.8534 (mtp) cc_final: 0.8080 (mtp) REVERT: G 34 MET cc_start: 0.9147 (mmm) cc_final: 0.8941 (mmm) REVERT: G 218 LYS cc_start: 0.9240 (pttt) cc_final: 0.8827 (tttp) REVERT: I 95 MET cc_start: 0.8031 (ttp) cc_final: 0.7336 (ttm) REVERT: I 104 MET cc_start: 0.8834 (ttt) cc_final: 0.8482 (ttp) REVERT: I 213 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8947 (tp) REVERT: I 467 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7871 (p) outliers start: 37 outliers final: 27 residues processed: 88 average time/residue: 0.3844 time to fit residues: 57.5575 Evaluate side-chains 83 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 2.902 ------------------------------------------------------------------------------- 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 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 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 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 257 THR Chi-restraints excluded: chain E residue 417 GLN Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 605 CYS 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 I residue 178 ASP Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain I residue 452 LEU Chi-restraints excluded: chain I residue 467 THR Chi-restraints excluded: chain I residue 475 MET Chi-restraints excluded: chain J residue 518 VAL Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 605 CYS Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 12 optimal weight: 0.0270 chunk 155 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 173 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 253 optimal weight: 0.0980 chunk 270 optimal weight: 2.9990 overall best weight: 2.6244 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** 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 = 0.3510 r_free = 0.3510 target = 0.039771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.029762 restraints weight = 252429.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.030544 restraints weight = 145208.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.031033 restraints weight = 105776.879| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25704 Z= 0.141 Angle : 0.636 9.387 35114 Z= 0.314 Chirality : 0.044 0.216 4119 Planarity : 0.004 0.049 4376 Dihedral : 7.957 58.804 4772 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 1.03 % Allowed : 10.83 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 3078 helix: 1.28 (0.26), residues: 468 sheet: -0.49 (0.16), residues: 1065 loop : -0.59 (0.17), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 112 HIS 0.007 0.001 HIS I 374 PHE 0.017 0.001 PHE E 376 TYR 0.019 0.001 TYR G 33 ARG 0.004 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00278 ( 34) link_NAG-ASN : angle 1.86531 ( 102) link_ALPHA1-6 : bond 0.00445 ( 6) link_ALPHA1-6 : angle 1.87997 ( 18) link_BETA1-4 : bond 0.00900 ( 23) link_BETA1-4 : angle 2.76591 ( 69) link_ALPHA1-3 : bond 0.00708 ( 6) link_ALPHA1-3 : angle 4.21365 ( 18) hydrogen bonds : bond 0.03476 ( 934) hydrogen bonds : angle 5.60447 ( 2574) SS BOND : bond 0.00241 ( 48) SS BOND : angle 0.69397 ( 96) covalent geometry : bond 0.00312 (25587) covalent geometry : angle 0.60854 (34811) *********************** 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 84 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9566 (mmtt) cc_final: 0.9200 (mmtm) REVERT: F 530 MET cc_start: 0.8541 (mtp) cc_final: 0.8097 (mtp) REVERT: G 218 LYS cc_start: 0.9255 (pttt) cc_final: 0.8789 (tptt) REVERT: I 95 MET cc_start: 0.7995 (ttp) cc_final: 0.7342 (ttm) REVERT: I 213 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (tp) REVERT: K 34 MET cc_start: 0.9035 (mmm) cc_final: 0.8787 (mmm) REVERT: K 218 LYS cc_start: 0.9260 (pttt) cc_final: 0.8816 (tptt) outliers start: 28 outliers final: 20 residues processed: 81 average time/residue: 0.3700 time to fit residues: 51.2069 Evaluate side-chains 74 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 2.949 ------------------------------------------------------------------------------- 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 540 GLN Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain C residue 143 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 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 215 ILE Chi-restraints excluded: chain I residue 257 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 122 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 256 optimal weight: 0.0030 chunk 44 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 112 optimal weight: 0.5980 chunk 241 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 182 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.040029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.030100 restraints weight = 250540.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.030905 restraints weight = 142705.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031407 restraints weight = 102922.394| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25704 Z= 0.110 Angle : 0.605 9.390 35114 Z= 0.299 Chirality : 0.044 0.214 4119 Planarity : 0.004 0.048 4376 Dihedral : 7.595 57.197 4772 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 0.88 % Allowed : 11.20 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.16), residues: 3078 helix: 1.42 (0.26), residues: 468 sheet: -0.50 (0.15), residues: 1101 loop : -0.50 (0.18), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 112 HIS 0.006 0.001 HIS I 374 PHE 0.016 0.001 PHE A 376 TYR 0.018 0.001 TYR G 33 ARG 0.003 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 34) link_NAG-ASN : angle 1.74696 ( 102) link_ALPHA1-6 : bond 0.00477 ( 6) link_ALPHA1-6 : angle 1.75467 ( 18) link_BETA1-4 : bond 0.00900 ( 23) link_BETA1-4 : angle 2.73541 ( 69) link_ALPHA1-3 : bond 0.00828 ( 6) link_ALPHA1-3 : angle 4.07791 ( 18) hydrogen bonds : bond 0.03196 ( 934) hydrogen bonds : angle 5.37552 ( 2574) SS BOND : bond 0.00231 ( 48) SS BOND : angle 0.66514 ( 96) covalent geometry : bond 0.00237 (25587) covalent geometry : angle 0.57814 (34811) *********************** 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 79 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: C 213 LYS cc_start: 0.9556 (mmtt) cc_final: 0.9191 (mmtm) REVERT: C 218 LYS cc_start: 0.9219 (pttt) cc_final: 0.8732 (tptt) REVERT: F 530 MET cc_start: 0.8678 (mtp) cc_final: 0.8286 (mtp) REVERT: G 218 LYS cc_start: 0.9253 (pttt) cc_final: 0.8792 (tptt) REVERT: I 95 MET cc_start: 0.7929 (ttp) cc_final: 0.7324 (ttm) REVERT: I 213 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8988 (tp) REVERT: I 434 MET cc_start: 0.8351 (ptm) cc_final: 0.8135 (ptm) REVERT: J 614 TRP cc_start: 0.6319 (OUTLIER) cc_final: 0.5835 (m-10) REVERT: K 34 MET cc_start: 0.9053 (mmm) cc_final: 0.8821 (mmm) REVERT: K 218 LYS cc_start: 0.9259 (pttt) cc_final: 0.8810 (tptt) outliers start: 24 outliers final: 21 residues processed: 77 average time/residue: 0.4109 time to fit residues: 54.8670 Evaluate side-chains 77 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 3.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 126 CYS 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 79 LEU Chi-restraints excluded: chain C residue 143 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 F residue 605 CYS 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 215 ILE Chi-restraints excluded: chain I residue 257 THR 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 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 51 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 22 optimal weight: 0.0270 chunk 160 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 213 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 overall best weight: 2.3244 ------------------------------------------------------------------------------- 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** ** E 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.039914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.029987 restraints weight = 252159.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.030770 restraints weight = 145264.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.031252 restraints weight = 105158.143| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3717 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= 0.128 Angle : 0.615 10.046 35114 Z= 0.302 Chirality : 0.044 0.207 4119 Planarity : 0.004 0.043 4376 Dihedral : 7.540 56.827 4772 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.62 % Favored : 94.12 % Rotamer: Outliers : 0.96 % Allowed : 11.01 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.16), residues: 3078 helix: 1.45 (0.26), residues: 468 sheet: -0.41 (0.15), residues: 1089 loop : -0.51 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 112 HIS 0.006 0.001 HIS I 374 PHE 0.015 0.001 PHE A 376 TYR 0.019 0.001 TYR G 33 ARG 0.004 0.000 ARG H 216 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 34) link_NAG-ASN : angle 1.79345 ( 102) link_ALPHA1-6 : bond 0.00411 ( 6) link_ALPHA1-6 : angle 1.87371 ( 18) link_BETA1-4 : bond 0.00884 ( 23) link_BETA1-4 : angle 2.74144 ( 69) link_ALPHA1-3 : bond 0.00780 ( 6) link_ALPHA1-3 : angle 3.87546 ( 18) hydrogen bonds : bond 0.03208 ( 934) hydrogen bonds : angle 5.33062 ( 2574) SS BOND : bond 0.00242 ( 48) SS BOND : angle 0.61103 ( 96) covalent geometry : bond 0.00284 (25587) covalent geometry : angle 0.58833 (34811) ********************** 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 80 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 6.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 213 LYS cc_start: 0.9554 (mmtt) cc_final: 0.9190 (mmtm) REVERT: C 218 LYS cc_start: 0.9215 (pttt) cc_final: 0.8734 (tptt) REVERT: F 530 MET cc_start: 0.8679 (mtp) cc_final: 0.8279 (mtp) REVERT: G 218 LYS cc_start: 0.9253 (pttt) cc_final: 0.8788 (tptt) REVERT: I 95 MET cc_start: 0.7954 (ttp) cc_final: 0.7375 (ttm) REVERT: I 213 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8936 (tp) REVERT: K 34 MET cc_start: 0.9056 (mmm) cc_final: 0.8829 (mmm) REVERT: K 218 LYS cc_start: 0.9233 (pttt) cc_final: 0.8769 (tptt) outliers start: 26 outliers final: 23 residues processed: 77 average time/residue: 0.3568 time to fit residues: 48.3565 Evaluate side-chains 78 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 126 CYS 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 79 LEU Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 126 CYS Chi-restraints excluded: chain I residue 213 ILE Chi-restraints excluded: chain I residue 215 ILE Chi-restraints excluded: chain I residue 257 THR 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 3 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 283 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 226 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 404 ASN ** 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** J 651 ASN L 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.039010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.029054 restraints weight = 251315.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.029787 restraints weight = 146303.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.030234 restraints weight = 107523.241| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3782 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= 0.313 Angle : 0.791 10.141 35114 Z= 0.385 Chirality : 0.048 0.230 4119 Planarity : 0.005 0.053 4376 Dihedral : 8.394 58.266 4771 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.59 % Rotamer: Outliers : 1.10 % Allowed : 11.16 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.16), residues: 3078 helix: 0.92 (0.25), residues: 468 sheet: -0.59 (0.15), residues: 1089 loop : -0.58 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 112 HIS 0.007 0.002 HIS I 330 PHE 0.024 0.002 PHE E 376 TYR 0.020 0.002 TYR E 61 ARG 0.005 0.001 ARG L 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00752 ( 34) link_NAG-ASN : angle 2.36245 ( 102) link_ALPHA1-6 : bond 0.00643 ( 6) link_ALPHA1-6 : angle 2.76507 ( 18) link_BETA1-4 : bond 0.01164 ( 23) link_BETA1-4 : angle 3.07114 ( 69) link_ALPHA1-3 : bond 0.00466 ( 6) link_ALPHA1-3 : angle 3.62364 ( 18) hydrogen bonds : bond 0.04228 ( 934) hydrogen bonds : angle 5.86902 ( 2574) SS BOND : bond 0.00384 ( 48) SS BOND : angle 0.97290 ( 96) covalent geometry : bond 0.00715 (25587) covalent geometry : angle 0.76326 (34811) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7933.09 seconds wall clock time: 141 minutes 32.21 seconds (8492.21 seconds total)