Starting phenix.real_space_refine on Thu Mar 5 04:41:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.map" model { file = "/net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p62_20259/03_2026/6p62_20259.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 132 5.16 5 C 12021 2.51 5 N 3171 2.21 5 O 3879 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19203 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "L" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "C" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "D" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "E" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4343 Classifications: {'peptide': 551} Link IDs: {'PTRANS': 23, 'TRANS': 527} Chain breaks: 5 Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 901 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 786 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "I" 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: "J" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "K" 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: "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: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "R" 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: "S" 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: "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: 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: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "X" 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: "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: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.49, per 1000 atoms: 0.23 Number of scatterers: 19203 At special positions: 0 Unit cell: (149.35, 149.35, 115.36, 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 132 16.00 O 3879 8.00 N 3171 7.00 C 12021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.11 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.10 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.06 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.11 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 433 " distance=2.01 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.10 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.04 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.04 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 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35A" - pdb=" SG CYS C 50 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.06 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.11 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.01 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.10 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN Q 4 " - " MAN Q 5 " " MAN Q 5 " - " MAN Q 6 " " MAN W 4 " - " MAN W 5 " " MAN W 5 " - " MAN W 6 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " ALPHA1-6 " BMA J 3 " - " MAN J 7 " " BMA Q 3 " - " MAN Q 7 " " BMA W 3 " - " MAN W 7 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 703 " - " ASN A 160 " " NAG A 704 " - " ASN A 197 " " NAG A 718 " - " ASN A 295 " " NAG A 719 " - " ASN A 301 " " NAG A 720 " - " ASN A 332 " " NAG A 721 " - " ASN A 133 " " NAG A 722 " - " ASN A 339 " " NAG A 727 " - " ASN A 392 " " NAG A 728 " - " ASN A 448 " " NAG B 703 " - " ASN B 160 " " NAG B 704 " - " ASN B 197 " " NAG B 718 " - " ASN B 295 " " NAG B 719 " - " ASN B 301 " " NAG B 720 " - " ASN B 332 " " NAG B 721 " - " ASN B 133 " " NAG B 722 " - " ASN B 339 " " NAG B 727 " - " ASN B 392 " " NAG B 728 " - " ASN B 448 " " NAG E 703 " - " ASN E 160 " " NAG E 704 " - " ASN E 197 " " NAG E 718 " - " ASN E 295 " " NAG E 719 " - " ASN E 301 " " NAG E 720 " - " ASN E 332 " " NAG E 721 " - " ASN E 133 " " NAG E 722 " - " ASN E 339 " " NAG E 727 " - " ASN E 392 " " NAG E 728 " - " ASN E 448 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN B 156 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 276 " " NAG T 1 " - " ASN B 363 " " NAG U 1 " - " ASN B 386 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 234 " " NAG X 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 363 " " NAG a 1 " - " ASN E 386 " Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 662.3 milliseconds 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4284 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 45 sheets defined 20.7% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.169A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.591A pdb=" N SER A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN A 543 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 544 " --> pdb=" O GLN A 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 546 " --> pdb=" O ARG A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 596 Processing helix chain 'A' and resid 611 through 615 Processing helix chain 'A' and resid 618 through 624 removed outlier: 3.907A pdb=" N ASP A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU A 647 " --> pdb=" O TYR A 643 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 648 " --> pdb=" O GLY A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 116 " --> pdb=" O TRP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 334 through 354 removed outlier: 3.864A pdb=" N LYS B 351 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.593A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.898A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 657 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.168A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.865A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.790A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.344A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 534 removed outlier: 3.592A pdb=" N SER E 534 " --> pdb=" O MET E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 3.893A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 544 " --> pdb=" O GLN E 540 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU E 545 " --> pdb=" O ALA E 541 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER E 546 " --> pdb=" O ARG E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 572 through 596 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.908A pdb=" N ASP E 624 " --> pdb=" O SER E 620 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.500A pdb=" N GLU E 647 " --> pdb=" O TYR E 643 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) Processing helix chain 'E' and resid 652 through 657 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 497 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR A 132 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.580A pdb=" N LEU H 18 " --> pdb=" O MET H 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.701A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TYR H 33 " --> pdb=" O TYR H 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AB7, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB8, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR B 132 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.828A pdb=" N GLY B 451 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL B 442 " --> pdb=" O CYS B 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS B 296 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG B 444 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N ILE B 294 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N VAL B 446 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 10.656A pdb=" N VAL B 292 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN B 448 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR B 290 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 450 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA B 316 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE B 309 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR B 318 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE B 307 " --> pdb=" O TYR B 318 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR B 320 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS B 305 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 301 " --> pdb=" O ILE B 323A" (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU C 18 " --> pdb=" O MET C 81 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS C 92 " --> pdb=" O TRP C 103 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ARG C 94 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N CYS C 50 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET C 35 " --> pdb=" O CYS C 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR C 52 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR C 33 " --> pdb=" O TYR C 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AD4, first strand: chain 'E' and resid 495 through 497 Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.781A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.320A pdb=" N CYS E 201 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.621A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 393 through 395 removed outlier: 6.527A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 3.829A pdb=" N GLY E 451 " --> pdb=" O LEU E 260 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N VAL E 442 " --> pdb=" O CYS E 296 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N CYS E 296 " --> pdb=" O VAL E 442 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.657A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 315 through 323A removed outlier: 6.943A pdb=" N ALA E 316 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE E 309 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.581A pdb=" N LEU F 18 " --> pdb=" O MET F 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.702A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR F 33 " --> pdb=" O TYR F 52 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AE8, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AE9, first strand: chain 'G' and resid 48 through 49 745 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5903 1.34 - 1.48: 5988 1.48 - 1.63: 7519 1.63 - 1.78: 83 1.78 - 1.93: 94 Bond restraints: 19587 Sorted by residual: bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.351 0.161 2.20e-02 2.07e+03 5.34e+01 bond pdb=" CB TYR D 36 " pdb=" CG TYR D 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.31e+01 bond pdb=" CB TYR G 36 " pdb=" CG TYR G 36 " ideal model delta sigma weight residual 1.512 1.352 0.160 2.20e-02 2.07e+03 5.29e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.09e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.397 0.100 1.40e-02 5.10e+03 5.08e+01 ... (remaining 19582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.82: 23757 2.82 - 5.64: 2539 5.64 - 8.46: 284 8.46 - 11.28: 36 11.28 - 14.10: 6 Bond angle restraints: 26622 Sorted by residual: angle pdb=" N ASP D 95B" pdb=" CA ASP D 95B" pdb=" C ASP D 95B" ideal model delta sigma weight residual 109.79 123.89 -14.10 1.56e+00 4.11e-01 8.17e+01 angle pdb=" N ASP G 95B" pdb=" CA ASP G 95B" pdb=" C ASP G 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.16e+01 angle pdb=" N ASP L 95B" pdb=" CA ASP L 95B" pdb=" C ASP L 95B" ideal model delta sigma weight residual 109.79 123.88 -14.09 1.56e+00 4.11e-01 8.15e+01 angle pdb=" N ARG G 61 " pdb=" CA ARG G 61 " pdb=" C ARG G 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.49e+01 angle pdb=" N ARG D 61 " pdb=" CA ARG D 61 " pdb=" C ARG D 61 " ideal model delta sigma weight residual 114.04 103.31 10.73 1.24e+00 6.50e-01 7.48e+01 ... (remaining 26617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 12245 21.72 - 43.45: 316 43.45 - 65.17: 108 65.17 - 86.90: 45 86.90 - 108.62: 24 Dihedral angle restraints: 12738 sinusoidal: 6063 harmonic: 6675 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 157 " pdb=" CB CYS B 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.36 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 157 " pdb=" CB CYS E 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.39 47.61 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 157 " pdb=" CB CYS A 157 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 ... (remaining 12735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2398 0.109 - 0.218: 751 0.218 - 0.326: 88 0.326 - 0.435: 6 0.435 - 0.544: 12 Chirality restraints: 3255 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.57e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.51e+01 ... (remaining 3252 not shown) Planarity restraints: 3318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN B 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN B 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN B 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG B 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN E 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG E 704 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.052 2.00e-02 2.50e+03 5.54e-02 3.84e+01 pdb=" CG ASN A 197 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A 704 " 0.067 2.00e-02 2.50e+03 ... (remaining 3315 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5208 2.80 - 3.32: 17127 3.32 - 3.85: 31345 3.85 - 4.37: 37289 4.37 - 4.90: 61179 Nonbonded interactions: 152148 Sorted by model distance: nonbonded pdb=" O PRO H 100F" pdb=" OH TYR L 36 " model vdw 2.272 3.040 nonbonded pdb=" O PRO C 100F" pdb=" OH TYR D 36 " model vdw 2.272 3.040 nonbonded pdb=" O PRO F 100F" pdb=" OH TYR G 36 " model vdw 2.272 3.040 nonbonded pdb=" O3 NAG Z 2 " pdb=" O7 NAG Z 2 " model vdw 2.363 3.040 nonbonded pdb=" O3 NAG T 2 " pdb=" O7 NAG T 2 " model vdw 2.363 3.040 ... (remaining 152143 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'K' selection = chain 'R' selection = chain 'X' } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.760 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.161 19710 Z= 1.203 Angle : 1.853 14.101 26952 Z= 1.169 Chirality : 0.103 0.544 3255 Planarity : 0.009 0.046 3273 Dihedral : 12.688 108.619 8337 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.15 % Allowed : 0.45 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.17), residues: 2286 helix: -0.34 (0.25), residues: 378 sheet: 0.04 (0.18), residues: 756 loop : -0.33 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 94 TYR 0.055 0.008 TYR L 92 PHE 0.044 0.007 PHE F 95 TRP 0.037 0.008 TRP E 479 HIS 0.013 0.003 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.02250 (19587) covalent geometry : angle 1.81388 (26622) SS BOND : bond 0.03129 ( 39) SS BOND : angle 3.88973 ( 78) hydrogen bonds : bond 0.18943 ( 679) hydrogen bonds : angle 8.29636 ( 1866) link_ALPHA1-2 : bond 0.03583 ( 6) link_ALPHA1-2 : angle 3.35880 ( 18) link_ALPHA1-3 : bond 0.03124 ( 6) link_ALPHA1-3 : angle 3.35031 ( 18) link_ALPHA1-6 : bond 0.04357 ( 3) link_ALPHA1-6 : angle 3.24349 ( 9) link_BETA1-4 : bond 0.02787 ( 24) link_BETA1-4 : angle 4.56762 ( 72) link_NAG-ASN : bond 0.03318 ( 45) link_NAG-ASN : angle 3.59965 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 578 time to evaluate : 0.714 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.7815 (p0) cc_final: 0.7528 (t0) REVERT: A 424 ILE cc_start: 0.9068 (pt) cc_final: 0.8786 (pt) REVERT: A 426 MET cc_start: 0.8732 (tpt) cc_final: 0.8520 (tpt) REVERT: A 577 GLN cc_start: 0.7460 (mt0) cc_final: 0.7252 (tp40) REVERT: H 2 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7440 (mp10) REVERT: H 75 THR cc_start: 0.7992 (p) cc_final: 0.7630 (t) REVERT: L 65 SER cc_start: 0.8756 (p) cc_final: 0.8476 (m) REVERT: B 130 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7196 (mm-40) REVERT: B 174 SER cc_start: 0.8911 (t) cc_final: 0.8642 (p) REVERT: B 302 TYR cc_start: 0.7788 (m-80) cc_final: 0.7575 (m-10) REVERT: C 77 VAL cc_start: 0.8581 (t) cc_final: 0.8322 (p) REVERT: D 8 PRO cc_start: 0.7436 (Cg_endo) cc_final: 0.7169 (Cg_exo) REVERT: D 65 SER cc_start: 0.8689 (p) cc_final: 0.8376 (m) REVERT: E 54 CYS cc_start: 0.8508 (p) cc_final: 0.8110 (m) REVERT: E 99 ASN cc_start: 0.7591 (p0) cc_final: 0.7321 (t0) REVERT: E 104 MET cc_start: 0.8587 (ttt) cc_final: 0.8373 (ttt) REVERT: E 174 SER cc_start: 0.8972 (t) cc_final: 0.8748 (p) REVERT: E 577 GLN cc_start: 0.7692 (mt0) cc_final: 0.7436 (tp40) REVERT: F 2 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7295 (mp10) REVERT: F 86 ASP cc_start: 0.8065 (m-30) cc_final: 0.7712 (m-30) REVERT: G 52 SER cc_start: 0.9125 (p) cc_final: 0.8921 (t) REVERT: G 65 SER cc_start: 0.8669 (p) cc_final: 0.8357 (m) REVERT: G 74 THR cc_start: 0.8638 (m) cc_final: 0.8431 (p) outliers start: 3 outliers final: 3 residues processed: 581 average time/residue: 0.1482 time to fit residues: 128.7262 Evaluate side-chains 323 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 320 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain E residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 246 GLN A 352 HIS A 478 ASN H 80 GLN B 103 GLN B 105 HIS B 352 HIS B 356 ASN B 425 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN E 105 HIS E 137 ASN E 352 HIS E 425 ASN E 428 GLN F 80 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.095556 restraints weight = 37444.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098429 restraints weight = 22713.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.100323 restraints weight = 16369.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.101631 restraints weight = 13104.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.102443 restraints weight = 11204.345| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19710 Z= 0.188 Angle : 0.853 13.144 26952 Z= 0.432 Chirality : 0.049 0.192 3255 Planarity : 0.005 0.041 3273 Dihedral : 9.544 62.768 4209 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.60 % Allowed : 8.40 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.17), residues: 2286 helix: 0.67 (0.28), residues: 384 sheet: -0.31 (0.18), residues: 732 loop : -0.67 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 298 TYR 0.017 0.002 TYR B 217 PHE 0.026 0.003 PHE H 95 TRP 0.018 0.002 TRP A 479 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00409 (19587) covalent geometry : angle 0.80192 (26622) SS BOND : bond 0.00620 ( 39) SS BOND : angle 1.70746 ( 78) hydrogen bonds : bond 0.06202 ( 679) hydrogen bonds : angle 6.34052 ( 1866) link_ALPHA1-2 : bond 0.00258 ( 6) link_ALPHA1-2 : angle 2.35906 ( 18) link_ALPHA1-3 : bond 0.00739 ( 6) link_ALPHA1-3 : angle 2.39557 ( 18) link_ALPHA1-6 : bond 0.01062 ( 3) link_ALPHA1-6 : angle 1.17611 ( 9) link_BETA1-4 : bond 0.00957 ( 24) link_BETA1-4 : angle 3.10952 ( 72) link_NAG-ASN : bond 0.00490 ( 45) link_NAG-ASN : angle 3.18875 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 372 time to evaluate : 0.706 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: A 130 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6936 (mm-40) REVERT: A 323 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8737 (pt) REVERT: L 65 SER cc_start: 0.8911 (p) cc_final: 0.8526 (m) REVERT: B 174 SER cc_start: 0.9163 (t) cc_final: 0.8640 (p) REVERT: C 23 LYS cc_start: 0.8400 (tttt) cc_final: 0.8012 (tptt) REVERT: C 75 THR cc_start: 0.7779 (p) cc_final: 0.7522 (p) REVERT: D 61 ARG cc_start: 0.6833 (mtp180) cc_final: 0.6532 (mtp180) REVERT: D 65 SER cc_start: 0.8815 (p) cc_final: 0.8498 (m) REVERT: D 77 ASP cc_start: 0.6616 (t0) cc_final: 0.6287 (t0) REVERT: E 130 GLN cc_start: 0.7619 (mm-40) cc_final: 0.6501 (mm-40) REVERT: E 174 SER cc_start: 0.9266 (t) cc_final: 0.8686 (p) REVERT: E 461 THR cc_start: 0.8522 (m) cc_final: 0.8290 (m) REVERT: E 530 MET cc_start: 0.7737 (mtp) cc_final: 0.7453 (mtp) REVERT: E 617 ARG cc_start: 0.7524 (mpt180) cc_final: 0.7143 (mpt180) REVERT: F 23 LYS cc_start: 0.8343 (tttt) cc_final: 0.7845 (tptt) REVERT: F 102 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8048 (mp) REVERT: G 65 SER cc_start: 0.8775 (p) cc_final: 0.8454 (m) REVERT: G 74 THR cc_start: 0.8839 (m) cc_final: 0.8535 (p) outliers start: 52 outliers final: 31 residues processed: 399 average time/residue: 0.1216 time to fit residues: 77.0911 Evaluate side-chains 322 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 576 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 220 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 GLN B 540 GLN B 575 GLN C 80 GLN E 478 ASN E 540 GLN E 575 GLN F 80 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090524 restraints weight = 37922.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093327 restraints weight = 22940.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.095219 restraints weight = 16665.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096514 restraints weight = 13384.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.097384 restraints weight = 11474.353| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 19710 Z= 0.229 Angle : 0.797 10.924 26952 Z= 0.401 Chirality : 0.047 0.202 3255 Planarity : 0.005 0.045 3273 Dihedral : 7.829 47.283 4209 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.75 % Allowed : 9.65 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2286 helix: 0.60 (0.28), residues: 387 sheet: -0.42 (0.18), residues: 747 loop : -0.92 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.018 0.002 TYR H 100 PHE 0.027 0.003 PHE C 95 TRP 0.012 0.002 TRP F 47 HIS 0.010 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00531 (19587) covalent geometry : angle 0.75018 (26622) SS BOND : bond 0.01159 ( 39) SS BOND : angle 1.90100 ( 78) hydrogen bonds : bond 0.05489 ( 679) hydrogen bonds : angle 5.98451 ( 1866) link_ALPHA1-2 : bond 0.00314 ( 6) link_ALPHA1-2 : angle 2.50179 ( 18) link_ALPHA1-3 : bond 0.00907 ( 6) link_ALPHA1-3 : angle 1.75456 ( 18) link_ALPHA1-6 : bond 0.01033 ( 3) link_ALPHA1-6 : angle 1.11731 ( 9) link_BETA1-4 : bond 0.00836 ( 24) link_BETA1-4 : angle 2.88623 ( 72) link_NAG-ASN : bond 0.00480 ( 45) link_NAG-ASN : angle 2.82903 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 294 time to evaluate : 0.758 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: A 244 THR cc_start: 0.9130 (t) cc_final: 0.8914 (m) REVERT: H 33 TYR cc_start: 0.8427 (m-80) cc_final: 0.8208 (m-80) REVERT: L 58 VAL cc_start: 0.7907 (t) cc_final: 0.7701 (t) REVERT: L 63 SER cc_start: 0.8991 (m) cc_final: 0.8534 (p) REVERT: L 65 SER cc_start: 0.8789 (p) cc_final: 0.8494 (m) REVERT: B 104 MET cc_start: 0.8861 (ttm) cc_final: 0.8508 (ttt) REVERT: B 652 GLN cc_start: 0.7217 (tp40) cc_final: 0.7014 (tp40) REVERT: D 61 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6877 (mtp85) REVERT: D 65 SER cc_start: 0.8776 (p) cc_final: 0.8487 (m) REVERT: D 74 THR cc_start: 0.8998 (m) cc_final: 0.8642 (p) REVERT: F 80 GLN cc_start: 0.7054 (mp-120) cc_final: 0.6841 (mp10) REVERT: G 65 SER cc_start: 0.8747 (p) cc_final: 0.8539 (m) outliers start: 75 outliers final: 47 residues processed: 340 average time/residue: 0.1259 time to fit residues: 68.2004 Evaluate side-chains 307 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 49 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 222 optimal weight: 0.2980 chunk 32 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS L 38 HIS E 130 GLN G 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.111786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.090416 restraints weight = 37901.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093199 restraints weight = 22531.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.095053 restraints weight = 16169.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096296 restraints weight = 12950.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097069 restraints weight = 11108.207| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19710 Z= 0.223 Angle : 0.763 10.278 26952 Z= 0.379 Chirality : 0.046 0.183 3255 Planarity : 0.005 0.046 3273 Dihedral : 7.026 40.552 4209 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.85 % Allowed : 9.90 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.17), residues: 2286 helix: 0.62 (0.28), residues: 387 sheet: -0.52 (0.18), residues: 780 loop : -1.10 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 38 TYR 0.020 0.002 TYR D 36 PHE 0.023 0.002 PHE A 522 TRP 0.028 0.002 TRP H 62 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00518 (19587) covalent geometry : angle 0.71968 (26622) SS BOND : bond 0.00997 ( 39) SS BOND : angle 1.63286 ( 78) hydrogen bonds : bond 0.05181 ( 679) hydrogen bonds : angle 5.84361 ( 1866) link_ALPHA1-2 : bond 0.00376 ( 6) link_ALPHA1-2 : angle 2.55975 ( 18) link_ALPHA1-3 : bond 0.00840 ( 6) link_ALPHA1-3 : angle 2.03821 ( 18) link_ALPHA1-6 : bond 0.00748 ( 3) link_ALPHA1-6 : angle 1.21896 ( 9) link_BETA1-4 : bond 0.00707 ( 24) link_BETA1-4 : angle 2.65626 ( 72) link_NAG-ASN : bond 0.00396 ( 45) link_NAG-ASN : angle 2.66994 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 281 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 63 SER cc_start: 0.8993 (m) cc_final: 0.8559 (p) REVERT: L 65 SER cc_start: 0.8677 (p) cc_final: 0.8435 (m) REVERT: L 105 VAL cc_start: 0.5942 (t) cc_final: 0.5704 (t) REVERT: B 104 MET cc_start: 0.8870 (ttm) cc_final: 0.8576 (ttt) REVERT: B 246 GLN cc_start: 0.6849 (pm20) cc_final: 0.6486 (tt0) REVERT: B 482 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7430 (mm-30) REVERT: B 530 MET cc_start: 0.7520 (mtp) cc_final: 0.7310 (mtp) REVERT: B 652 GLN cc_start: 0.7288 (tp40) cc_final: 0.6987 (tp40) REVERT: D 61 ARG cc_start: 0.7279 (mtp180) cc_final: 0.6924 (mtp85) REVERT: D 77 ASP cc_start: 0.6753 (t0) cc_final: 0.6373 (t0) REVERT: D 105 VAL cc_start: 0.6329 (t) cc_final: 0.5783 (m) REVERT: E 482 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7634 (mm-30) REVERT: F 80 GLN cc_start: 0.6947 (mp-120) cc_final: 0.6740 (mp10) REVERT: F 86 ASP cc_start: 0.7735 (m-30) cc_final: 0.7357 (m-30) REVERT: G 33 VAL cc_start: 0.8902 (t) cc_final: 0.8645 (t) outliers start: 77 outliers final: 58 residues processed: 328 average time/residue: 0.1235 time to fit residues: 65.5225 Evaluate side-chains 309 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 27 ILE Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 146 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN B 540 GLN E 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.091070 restraints weight = 37430.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093809 restraints weight = 22761.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095680 restraints weight = 16575.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.096947 restraints weight = 13310.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097817 restraints weight = 11437.530| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19710 Z= 0.153 Angle : 0.694 11.829 26952 Z= 0.343 Chirality : 0.045 0.257 3255 Planarity : 0.004 0.049 3273 Dihedral : 6.391 38.182 4207 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.40 % Allowed : 11.09 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.17), residues: 2286 helix: 0.91 (0.29), residues: 369 sheet: -0.49 (0.18), residues: 777 loop : -1.26 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.019 0.001 TYR D 36 PHE 0.014 0.002 PHE H 95 TRP 0.014 0.001 TRP F 62 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00351 (19587) covalent geometry : angle 0.65253 (26622) SS BOND : bond 0.00547 ( 39) SS BOND : angle 1.59747 ( 78) hydrogen bonds : bond 0.04602 ( 679) hydrogen bonds : angle 5.65812 ( 1866) link_ALPHA1-2 : bond 0.00160 ( 6) link_ALPHA1-2 : angle 2.30042 ( 18) link_ALPHA1-3 : bond 0.00970 ( 6) link_ALPHA1-3 : angle 1.66333 ( 18) link_ALPHA1-6 : bond 0.00651 ( 3) link_ALPHA1-6 : angle 1.43685 ( 9) link_BETA1-4 : bond 0.00849 ( 24) link_BETA1-4 : angle 2.49535 ( 72) link_NAG-ASN : bond 0.00330 ( 45) link_NAG-ASN : angle 2.48317 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7825 (tm-30) REVERT: H 101 ASP cc_start: 0.8232 (t0) cc_final: 0.7984 (t0) REVERT: L 63 SER cc_start: 0.8914 (m) cc_final: 0.8529 (p) REVERT: L 65 SER cc_start: 0.8653 (p) cc_final: 0.8363 (m) REVERT: B 104 MET cc_start: 0.8848 (ttm) cc_final: 0.8536 (ttt) REVERT: B 482 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7443 (mm-30) REVERT: B 530 MET cc_start: 0.7498 (mtp) cc_final: 0.7235 (mtp) REVERT: B 652 GLN cc_start: 0.7358 (tp40) cc_final: 0.7066 (tp40) REVERT: E 482 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7609 (mm-30) REVERT: E 651 ASN cc_start: 0.7503 (m-40) cc_final: 0.7154 (t0) REVERT: F 86 ASP cc_start: 0.7720 (m-30) cc_final: 0.7334 (m-30) REVERT: G 61 ARG cc_start: 0.7908 (mtm110) cc_final: 0.7574 (mtp85) REVERT: G 77 ASP cc_start: 0.6760 (t0) cc_final: 0.6339 (t0) REVERT: G 105 VAL cc_start: 0.6527 (t) cc_final: 0.6304 (m) outliers start: 68 outliers final: 51 residues processed: 324 average time/residue: 0.1141 time to fit residues: 60.6981 Evaluate side-chains 306 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 196 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 202 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN F 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.115607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093602 restraints weight = 37139.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096416 restraints weight = 22528.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098315 restraints weight = 16208.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.099584 restraints weight = 12992.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100457 restraints weight = 11139.745| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19710 Z= 0.120 Angle : 0.647 14.835 26952 Z= 0.318 Chirality : 0.044 0.334 3255 Planarity : 0.004 0.049 3273 Dihedral : 5.760 36.377 4207 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.00 % Allowed : 11.94 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2286 helix: 1.11 (0.29), residues: 363 sheet: -0.31 (0.18), residues: 795 loop : -1.32 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.022 0.001 TYR G 67 PHE 0.017 0.001 PHE A 522 TRP 0.017 0.001 TRP E 571 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00264 (19587) covalent geometry : angle 0.61003 (26622) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.39296 ( 78) hydrogen bonds : bond 0.04077 ( 679) hydrogen bonds : angle 5.45048 ( 1866) link_ALPHA1-2 : bond 0.00202 ( 6) link_ALPHA1-2 : angle 2.04134 ( 18) link_ALPHA1-3 : bond 0.00892 ( 6) link_ALPHA1-3 : angle 1.39028 ( 18) link_ALPHA1-6 : bond 0.00459 ( 3) link_ALPHA1-6 : angle 1.42193 ( 9) link_BETA1-4 : bond 0.00820 ( 24) link_BETA1-4 : angle 2.28403 ( 72) link_NAG-ASN : bond 0.00344 ( 45) link_NAG-ASN : angle 2.30796 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 271 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7827 (tm-30) REVERT: L 63 SER cc_start: 0.8975 (m) cc_final: 0.8585 (p) REVERT: L 65 SER cc_start: 0.8624 (p) cc_final: 0.8243 (m) REVERT: B 104 MET cc_start: 0.8829 (ttm) cc_final: 0.8545 (ttt) REVERT: B 466 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 482 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7385 (mm-30) REVERT: B 619 LEU cc_start: 0.7430 (mt) cc_final: 0.7213 (mm) REVERT: B 652 GLN cc_start: 0.7153 (tp40) cc_final: 0.6915 (tp40) REVERT: E 482 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7501 (mm-30) REVERT: F 86 ASP cc_start: 0.7588 (m-30) cc_final: 0.7213 (m-30) REVERT: G 61 ARG cc_start: 0.7857 (mtm110) cc_final: 0.7547 (mtp85) REVERT: G 77 ASP cc_start: 0.6843 (t0) cc_final: 0.6603 (t0) outliers start: 60 outliers final: 46 residues processed: 313 average time/residue: 0.1159 time to fit residues: 59.5283 Evaluate side-chains 286 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 124 optimal weight: 5.9990 chunk 198 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 101 optimal weight: 0.0470 chunk 194 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 161 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN D 37 GLN E 88 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN G 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090903 restraints weight = 37542.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093667 restraints weight = 23017.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095527 restraints weight = 16669.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096737 restraints weight = 13435.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097601 restraints weight = 11582.601| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19710 Z= 0.172 Angle : 0.700 15.308 26952 Z= 0.342 Chirality : 0.046 0.505 3255 Planarity : 0.004 0.051 3273 Dihedral : 5.905 40.149 4207 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.40 % Allowed : 12.19 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.17), residues: 2286 helix: 1.10 (0.29), residues: 363 sheet: -0.35 (0.19), residues: 780 loop : -1.37 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.022 0.001 TYR G 67 PHE 0.017 0.002 PHE H 95 TRP 0.018 0.001 TRP E 571 HIS 0.003 0.001 HIS L 38 Details of bonding type rmsd covalent geometry : bond 0.00401 (19587) covalent geometry : angle 0.66183 (26622) SS BOND : bond 0.00526 ( 39) SS BOND : angle 1.45411 ( 78) hydrogen bonds : bond 0.04445 ( 679) hydrogen bonds : angle 5.51722 ( 1866) link_ALPHA1-2 : bond 0.00111 ( 6) link_ALPHA1-2 : angle 2.36089 ( 18) link_ALPHA1-3 : bond 0.00820 ( 6) link_ALPHA1-3 : angle 1.67866 ( 18) link_ALPHA1-6 : bond 0.00504 ( 3) link_ALPHA1-6 : angle 1.41161 ( 9) link_BETA1-4 : bond 0.00775 ( 24) link_BETA1-4 : angle 2.41560 ( 72) link_NAG-ASN : bond 0.00379 ( 45) link_NAG-ASN : angle 2.43248 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 249 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 478 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8306 (t0) REVERT: H 2 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7202 (mp10) REVERT: L 63 SER cc_start: 0.9008 (m) cc_final: 0.8659 (p) REVERT: L 65 SER cc_start: 0.8581 (p) cc_final: 0.8237 (m) REVERT: B 104 MET cc_start: 0.8856 (ttm) cc_final: 0.8580 (ttt) REVERT: B 482 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 651 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6995 (t0) REVERT: B 652 GLN cc_start: 0.7441 (tp40) cc_final: 0.7116 (tp40) REVERT: C 7 SER cc_start: 0.8092 (OUTLIER) cc_final: 0.7231 (m) REVERT: C 35 MET cc_start: 0.7359 (mmm) cc_final: 0.7002 (tpp) REVERT: E 482 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7521 (mm-30) REVERT: F 2 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7302 (mp10) outliers start: 68 outliers final: 53 residues processed: 290 average time/residue: 0.1143 time to fit residues: 55.2630 Evaluate side-chains 294 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 95 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 8.9990 chunk 194 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 651 ASN E 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.114902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.092674 restraints weight = 37397.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.095451 restraints weight = 22829.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097337 restraints weight = 16557.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098606 restraints weight = 13276.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099422 restraints weight = 11389.022| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19710 Z= 0.127 Angle : 0.666 13.655 26952 Z= 0.326 Chirality : 0.044 0.420 3255 Planarity : 0.004 0.050 3273 Dihedral : 5.663 37.669 4207 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.90 % Allowed : 12.64 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2286 helix: 1.18 (0.29), residues: 363 sheet: -0.26 (0.19), residues: 795 loop : -1.41 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 28 TYR 0.020 0.001 TYR G 67 PHE 0.013 0.001 PHE H 95 TRP 0.012 0.001 TRP E 69 HIS 0.002 0.001 HIS D 38 Details of bonding type rmsd covalent geometry : bond 0.00285 (19587) covalent geometry : angle 0.63120 (26622) SS BOND : bond 0.00514 ( 39) SS BOND : angle 1.43191 ( 78) hydrogen bonds : bond 0.04079 ( 679) hydrogen bonds : angle 5.41241 ( 1866) link_ALPHA1-2 : bond 0.00208 ( 6) link_ALPHA1-2 : angle 2.06406 ( 18) link_ALPHA1-3 : bond 0.00859 ( 6) link_ALPHA1-3 : angle 1.36891 ( 18) link_ALPHA1-6 : bond 0.00437 ( 3) link_ALPHA1-6 : angle 1.42710 ( 9) link_BETA1-4 : bond 0.00822 ( 24) link_BETA1-4 : angle 2.27100 ( 72) link_NAG-ASN : bond 0.00318 ( 45) link_NAG-ASN : angle 2.27241 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 250 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8037 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 246 GLN cc_start: 0.7102 (pm20) cc_final: 0.6865 (pm20) REVERT: A 478 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8238 (t0) REVERT: H 2 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7182 (mp10) REVERT: H 81 MET cc_start: 0.6618 (mtm) cc_final: 0.6279 (mtm) REVERT: L 63 SER cc_start: 0.8989 (m) cc_final: 0.8646 (p) REVERT: L 65 SER cc_start: 0.8570 (p) cc_final: 0.8201 (m) REVERT: B 104 MET cc_start: 0.8845 (ttm) cc_final: 0.8555 (ttt) REVERT: B 482 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7334 (mm-30) REVERT: B 650 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7064 (mp10) REVERT: C 2 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7450 (mp10) REVERT: C 81 MET cc_start: 0.6744 (mtm) cc_final: 0.6394 (mtt) REVERT: E 482 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7461 (mm-30) REVERT: F 2 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7292 (mp10) REVERT: F 86 ASP cc_start: 0.7658 (m-30) cc_final: 0.7252 (m-30) REVERT: G 33 VAL cc_start: 0.8829 (t) cc_final: 0.8620 (t) REVERT: G 61 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7672 (mtm180) outliers start: 58 outliers final: 48 residues processed: 288 average time/residue: 0.1178 time to fit residues: 56.0824 Evaluate side-chains 283 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 650 GLN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 180 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 211 optimal weight: 0.5980 chunk 63 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091017 restraints weight = 37440.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093753 restraints weight = 22891.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.095585 restraints weight = 16667.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096795 restraints weight = 13449.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097671 restraints weight = 11626.124| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19710 Z= 0.166 Angle : 0.701 17.247 26952 Z= 0.342 Chirality : 0.045 0.348 3255 Planarity : 0.004 0.050 3273 Dihedral : 5.749 39.681 4207 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.00 % Allowed : 13.24 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.17), residues: 2286 helix: 1.11 (0.29), residues: 363 sheet: -0.32 (0.19), residues: 795 loop : -1.47 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.024 0.001 TYR G 67 PHE 0.017 0.002 PHE H 95 TRP 0.038 0.001 TRP B 571 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00388 (19587) covalent geometry : angle 0.66570 (26622) SS BOND : bond 0.00534 ( 39) SS BOND : angle 1.45973 ( 78) hydrogen bonds : bond 0.04292 ( 679) hydrogen bonds : angle 5.50365 ( 1866) link_ALPHA1-2 : bond 0.00064 ( 6) link_ALPHA1-2 : angle 2.32136 ( 18) link_ALPHA1-3 : bond 0.00788 ( 6) link_ALPHA1-3 : angle 1.56424 ( 18) link_ALPHA1-6 : bond 0.00471 ( 3) link_ALPHA1-6 : angle 1.43388 ( 9) link_BETA1-4 : bond 0.00743 ( 24) link_BETA1-4 : angle 2.34331 ( 72) link_NAG-ASN : bond 0.00313 ( 45) link_NAG-ASN : angle 2.33067 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 478 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8303 (t0) REVERT: H 2 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7200 (mp10) REVERT: H 81 MET cc_start: 0.6713 (mtm) cc_final: 0.6499 (mtm) REVERT: L 63 SER cc_start: 0.9020 (m) cc_final: 0.8679 (p) REVERT: L 65 SER cc_start: 0.8556 (p) cc_final: 0.8150 (m) REVERT: L 105 VAL cc_start: 0.6404 (t) cc_final: 0.5831 (t) REVERT: B 104 MET cc_start: 0.8846 (ttm) cc_final: 0.8576 (ttt) REVERT: B 482 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7355 (mm-30) REVERT: B 571 TRP cc_start: 0.6173 (m100) cc_final: 0.5051 (m100) REVERT: B 651 ASN cc_start: 0.7163 (OUTLIER) cc_final: 0.6792 (t0) REVERT: C 2 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7378 (mp10) REVERT: C 35 MET cc_start: 0.7483 (tpp) cc_final: 0.7281 (mmm) REVERT: C 81 MET cc_start: 0.6721 (mtm) cc_final: 0.6246 (mtm) REVERT: E 482 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7467 (mm-30) REVERT: F 2 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7300 (mp10) REVERT: G 33 VAL cc_start: 0.8874 (t) cc_final: 0.8668 (t) outliers start: 60 outliers final: 54 residues processed: 285 average time/residue: 0.1135 time to fit residues: 53.6348 Evaluate side-chains 294 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092063 restraints weight = 37616.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094820 restraints weight = 22903.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096661 restraints weight = 16591.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097923 restraints weight = 13342.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098789 restraints weight = 11445.018| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19710 Z= 0.145 Angle : 0.685 16.238 26952 Z= 0.335 Chirality : 0.044 0.336 3255 Planarity : 0.004 0.050 3273 Dihedral : 5.686 38.670 4207 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.95 % Allowed : 13.39 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.17), residues: 2286 helix: 1.14 (0.29), residues: 363 sheet: -0.25 (0.19), residues: 789 loop : -1.52 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.023 0.001 TYR G 67 PHE 0.015 0.002 PHE H 95 TRP 0.028 0.001 TRP B 571 HIS 0.002 0.001 HIS G 38 Details of bonding type rmsd covalent geometry : bond 0.00335 (19587) covalent geometry : angle 0.65022 (26622) SS BOND : bond 0.00497 ( 39) SS BOND : angle 1.42370 ( 78) hydrogen bonds : bond 0.04171 ( 679) hydrogen bonds : angle 5.45378 ( 1866) link_ALPHA1-2 : bond 0.00118 ( 6) link_ALPHA1-2 : angle 2.16792 ( 18) link_ALPHA1-3 : bond 0.00813 ( 6) link_ALPHA1-3 : angle 1.41960 ( 18) link_ALPHA1-6 : bond 0.00433 ( 3) link_ALPHA1-6 : angle 1.45242 ( 9) link_BETA1-4 : bond 0.00784 ( 24) link_BETA1-4 : angle 2.29752 ( 72) link_NAG-ASN : bond 0.00307 ( 45) link_NAG-ASN : angle 2.29291 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4572 Ramachandran restraints generated. 2286 Oldfield, 0 Emsley, 2286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 478 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8281 (t0) REVERT: A 530 MET cc_start: 0.8095 (mmm) cc_final: 0.7844 (mtt) REVERT: H 2 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7132 (mp10) REVERT: H 99 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6642 (tmm-80) REVERT: L 63 SER cc_start: 0.9010 (m) cc_final: 0.8712 (p) REVERT: B 104 MET cc_start: 0.8818 (ttm) cc_final: 0.8528 (ttt) REVERT: B 482 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7399 (mm-30) REVERT: C 2 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7390 (mp10) REVERT: C 35 MET cc_start: 0.7437 (tpp) cc_final: 0.7226 (mmm) REVERT: C 52 LEU cc_start: 0.7908 (mp) cc_final: 0.7671 (mp) REVERT: C 81 MET cc_start: 0.6700 (mtm) cc_final: 0.6213 (mtm) REVERT: E 482 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 2 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7263 (mp10) outliers start: 59 outliers final: 50 residues processed: 280 average time/residue: 0.1117 time to fit residues: 52.3438 Evaluate side-chains 290 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 238 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 595 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 99 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 447 SER Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 20 THR Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 105 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.093766 restraints weight = 37344.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096589 restraints weight = 22838.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.098481 restraints weight = 16513.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099742 restraints weight = 13264.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.100622 restraints weight = 11407.053| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19710 Z= 0.120 Angle : 0.654 16.227 26952 Z= 0.322 Chirality : 0.043 0.312 3255 Planarity : 0.004 0.051 3273 Dihedral : 5.385 36.572 4207 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.35 % Allowed : 14.19 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.18), residues: 2286 helix: 1.20 (0.29), residues: 363 sheet: -0.17 (0.19), residues: 795 loop : -1.44 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.021 0.001 TYR G 67 PHE 0.014 0.001 PHE H 95 TRP 0.041 0.001 TRP B 571 HIS 0.002 0.001 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.00269 (19587) covalent geometry : angle 0.62220 (26622) SS BOND : bond 0.00471 ( 39) SS BOND : angle 1.38019 ( 78) hydrogen bonds : bond 0.03864 ( 679) hydrogen bonds : angle 5.37159 ( 1866) link_ALPHA1-2 : bond 0.00259 ( 6) link_ALPHA1-2 : angle 1.94006 ( 18) link_ALPHA1-3 : bond 0.00811 ( 6) link_ALPHA1-3 : angle 1.28625 ( 18) link_ALPHA1-6 : bond 0.00419 ( 3) link_ALPHA1-6 : angle 1.42431 ( 9) link_BETA1-4 : bond 0.00805 ( 24) link_BETA1-4 : angle 2.16908 ( 72) link_NAG-ASN : bond 0.00320 ( 45) link_NAG-ASN : angle 2.15415 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2950.28 seconds wall clock time: 52 minutes 11.88 seconds (3131.88 seconds total)