Starting phenix.real_space_refine on Sat Sep 12 23:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.cif Found real_map, /net/cci-nas-00/data/ceres_data/6p62_20259/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_2026/6p62_20259.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6p62_20259/09_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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 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 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 chiralities: 9 Time building chain proxies: 4.58, per 1000 atoms: 0.24 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: 1.84 Conformation dependent library (CDL) restraints added in 775.5 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: 0.73 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: 4.13 Time building geometry restraints manager: 2.29 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 - 16.70: 10587 16.70 - 33.40: 285 33.40 - 50.10: 81 50.10 - 66.80: 48 66.80 - 83.50: 15 Dihedral angle restraints: 11016 sinusoidal: 4341 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 11013 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: 0.05 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.180 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 9.850 83.504 6615 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/Z covalent geometry : bond 0.02250 / 1.20 (19587) covalent geometry : angle 1.81388 / 1.17 (26622) SS BOND : bond 0.03129 / 1.99 ( 39) SS BOND : angle 3.88973 / 2.49 ( 78) hydrogen bonds : bond 0.18943 / 12.84 ( 679) hydrogen bonds : angle 8.29636 / 5.75 ( 1866) link_ALPHA1-2 : bond 0.03583 / 1.76 ( 6) link_ALPHA1-2 : angle 3.35880 / 1.92 ( 18) link_ALPHA1-3 : bond 0.03124 / 1.54 ( 6) link_ALPHA1-3 : angle 3.35031 / 1.92 ( 18) link_ALPHA1-6 : bond 0.04357 / 2.01 ( 3) link_ALPHA1-6 : angle 3.24349 / 1.85 ( 9) link_BETA1-4 : bond 0.02787 / 1.83 ( 24) link_BETA1-4 : angle 4.56762 / 3.07 ( 72) link_NAG-ASN : bond 0.03318 / 2.07 ( 45) link_NAG-ASN : angle 3.59965 / 2.51 ( 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 : 0.724 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: 0.1511 time to fit residues: 132.5257 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 : 0.766 ------------------------------------------------------------------------------- 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... ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095649 restraints weight = 37422.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098537 restraints weight = 22833.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.100455 restraints weight = 16405.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101757 restraints weight = 13142.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102614 restraints weight = 11245.891| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3008 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= 0.181 Angle : 0.829 12.316 26952 Z= 0.422 Chirality : 0.048 0.195 3255 Planarity : 0.005 0.040 3273 Dihedral : 5.770 41.700 2487 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.55 % Allowed : 8.45 % 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: -0.52 (0.17), residues: 2286 helix: 0.66 (0.28), residues: 384 sheet: -0.29 (0.18), residues: 702 loop : -0.65 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 298 TYR 0.019 0.002 TYR B 217 PHE 0.026 0.003 PHE H 95 TRP 0.018 0.002 TRP A 479 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (19587) covalent geometry : angle 0.78010 / 0.41 (26622) SS BOND : bond 0.00578 / 0.38 ( 39) SS BOND : angle 1.84195 / 1.17 ( 78) hydrogen bonds : bond 0.06030 / 4.11 ( 679) hydrogen bonds : angle 6.33411 / 4.43 ( 1866) link_ALPHA1-2 : bond 0.00229 / 0.12 ( 6) link_ALPHA1-2 : angle 2.07683 / 1.29 ( 18) link_ALPHA1-3 : bond 0.00228 / 0.12 ( 6) link_ALPHA1-3 : angle 1.59548 / 1.02 ( 18) link_ALPHA1-6 : bond 0.00877 / 0.41 ( 3) link_ALPHA1-6 : angle 1.07473 / 0.54 ( 9) link_BETA1-4 : bond 0.00861 / 0.59 ( 24) link_BETA1-4 : angle 2.81323 / 1.94 ( 72) link_NAG-ASN : bond 0.00505 / 0.31 ( 45) link_NAG-ASN : angle 3.15609 / 2.29 ( 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: 51 poor density : 373 time to evaluate : 0.750 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: 0.7410 (mm-40) cc_final: 0.6929 (mm-40) REVERT: A 161 MET cc_start: 0.8269 (tpt) cc_final: 0.8002 (tpt) REVERT: A 323 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8741 (pt) REVERT: L 65 SER cc_start: 0.8908 (p) cc_final: 0.8533 (m) REVERT: C 23 LYS cc_start: 0.8406 (tttt) cc_final: 0.8017 (tptt) REVERT: C 75 THR cc_start: 0.7778 (p) cc_final: 0.7500 (p) REVERT: D 61 ARG cc_start: 0.6893 (mtp180) cc_final: 0.6609 (mtp180) REVERT: D 65 SER cc_start: 0.8806 (p) cc_final: 0.8492 (m) REVERT: D 77 ASP cc_start: 0.6576 (t0) cc_final: 0.6266 (t0) REVERT: E 130 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6481 (mm-40) REVERT: E 461 THR cc_start: 0.8511 (m) cc_final: 0.8297 (m) REVERT: E 530 MET cc_start: 0.7729 (mtp) cc_final: 0.7462 (mtp) REVERT: E 617 ARG cc_start: 0.7408 (mpt180) cc_final: 0.7068 (mpt180) REVERT: F 23 LYS cc_start: 0.8329 (tttt) cc_final: 0.7831 (tptt) REVERT: F 80 GLN cc_start: 0.7070 (mp10) cc_final: 0.6824 (mp10) REVERT: F 102 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8101 (mp) REVERT: G 12 GLU cc_start: 0.7339 (tp30) cc_final: 0.6979 (tp30) REVERT: G 65 SER cc_start: 0.8790 (p) cc_final: 0.8482 (m) REVERT: G 74 THR cc_start: 0.8879 (m) cc_final: 0.8581 (p) outliers start: 51 outliers final: 30 residues processed: 400 average time/residue: 0.1333 time to fit residues: 84.7626 Evaluate side-chains 316 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 7 THR 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 51 ILE 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: 5.9990 chunk 59 optimal weight: 0.0970 chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 HIS H 80 GLN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN C 80 GLN E 478 ASN E 540 GLN E 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.116110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094111 restraints weight = 37937.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.096961 restraints weight = 23120.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.098870 restraints weight = 16661.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100169 restraints weight = 13342.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.101049 restraints weight = 11422.310| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19710 Z= 0.165 Angle : 0.731 10.760 26952 Z= 0.369 Chirality : 0.045 0.218 3255 Planarity : 0.004 0.043 3273 Dihedral : 5.424 39.354 2487 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.35 % Allowed : 10.14 % Favored : 86.51 % 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: -0.57 (0.17), residues: 2286 helix: 0.70 (0.28), residues: 387 sheet: -0.07 (0.19), residues: 690 loop : -0.88 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 298 TYR 0.015 0.002 TYR F 100 PHE 0.020 0.002 PHE C 95 TRP 0.011 0.001 TRP C 62 HIS 0.008 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (19587) covalent geometry : angle 0.68789 / 0.36 (26622) SS BOND : bond 0.00691 / 0.47 ( 39) SS BOND : angle 1.76804 / 1.16 ( 78) hydrogen bonds : bond 0.05089 / 3.48 ( 679) hydrogen bonds : angle 5.89566 / 4.11 ( 1866) link_ALPHA1-2 : bond 0.00197 / 0.11 ( 6) link_ALPHA1-2 : angle 2.01154 / 1.24 ( 18) link_ALPHA1-3 : bond 0.00365 / 0.18 ( 6) link_ALPHA1-3 : angle 1.51669 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00877 / 0.40 ( 3) link_ALPHA1-6 : angle 1.15535 / 0.57 ( 9) link_BETA1-4 : bond 0.00866 / 0.61 ( 24) link_BETA1-4 : angle 2.49727 / 1.73 ( 72) link_NAG-ASN : bond 0.00361 / 0.22 ( 45) link_NAG-ASN : angle 2.72568 / 1.99 ( 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 361 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8274 (tpt) cc_final: 0.8045 (tpt) REVERT: A 244 THR cc_start: 0.9121 (t) cc_final: 0.8895 (m) REVERT: H 62 TRP cc_start: 0.7655 (p-90) cc_final: 0.6854 (p-90) REVERT: L 63 SER cc_start: 0.8986 (m) cc_final: 0.8530 (p) REVERT: L 65 SER cc_start: 0.8779 (p) cc_final: 0.8447 (m) REVERT: B 104 MET cc_start: 0.8772 (ttm) cc_final: 0.8467 (ttt) REVERT: B 619 LEU cc_start: 0.7444 (mt) cc_final: 0.7200 (mm) REVERT: D 61 ARG cc_start: 0.6913 (mtp180) cc_final: 0.6636 (mtp85) REVERT: D 65 SER cc_start: 0.8764 (p) cc_final: 0.8442 (m) REVERT: G 33 VAL cc_start: 0.8693 (t) cc_final: 0.8464 (t) REVERT: G 65 SER cc_start: 0.8718 (p) cc_final: 0.8483 (m) outliers start: 67 outliers final: 41 residues processed: 340 average time/residue: 0.1326 time to fit residues: 72.3546 Evaluate side-chains 293 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL 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 20 LEU 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 95 ASP Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 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 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 108 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 7 THR 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: 8.9990 chunk 140 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 222 optimal weight: 0.0020 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 HIS B 540 GLN E 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.091892 restraints weight = 37743.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094741 restraints weight = 22449.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096634 restraints weight = 16021.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097905 restraints weight = 12767.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098725 restraints weight = 10919.699| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19710 Z= 0.201 Angle : 0.746 10.764 26952 Z= 0.373 Chirality : 0.045 0.238 3255 Planarity : 0.004 0.043 3273 Dihedral : 5.341 37.210 2487 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.75 % Allowed : 10.24 % Favored : 86.01 % 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: -0.82 (0.17), residues: 2286 helix: 0.70 (0.28), residues: 387 sheet: -0.45 (0.18), residues: 786 loop : -1.00 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 617 TYR 0.019 0.002 TYR D 36 PHE 0.024 0.002 PHE A 522 TRP 0.019 0.002 TRP F 62 HIS 0.004 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (19587) covalent geometry : angle 0.70577 / 0.36 (26622) SS BOND : bond 0.00581 / 0.38 ( 39) SS BOND : angle 1.56155 / 1.01 ( 78) hydrogen bonds : bond 0.05053 / 3.45 ( 679) hydrogen bonds : angle 5.78193 / 4.05 ( 1866) link_ALPHA1-2 : bond 0.00253 / 0.12 ( 6) link_ALPHA1-2 : angle 2.29895 / 1.44 ( 18) link_ALPHA1-3 : bond 0.00212 / 0.12 ( 6) link_ALPHA1-3 : angle 1.69539 / 1.11 ( 18) link_ALPHA1-6 : bond 0.00741 / 0.34 ( 3) link_ALPHA1-6 : angle 1.10112 / 0.56 ( 9) link_BETA1-4 : bond 0.00676 / 0.47 ( 24) link_BETA1-4 : angle 2.47325 / 1.73 ( 72) link_NAG-ASN : bond 0.00436 / 0.27 ( 45) link_NAG-ASN : angle 2.64015 / 1.90 ( 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 356 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 281 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 62 TRP cc_start: 0.7813 (p-90) cc_final: 0.7494 (p-90) REVERT: H 99 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8124 (mmm160) REVERT: L 63 SER cc_start: 0.8987 (m) cc_final: 0.8553 (p) REVERT: L 65 SER cc_start: 0.8710 (p) cc_final: 0.8431 (m) REVERT: B 104 MET cc_start: 0.8811 (ttm) cc_final: 0.8473 (ttt) REVERT: B 323 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8863 (tt) REVERT: B 482 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7436 (mm-30) REVERT: D 61 ARG cc_start: 0.7173 (mtp180) cc_final: 0.6871 (mtp85) REVERT: D 77 ASP cc_start: 0.6571 (t0) cc_final: 0.6185 (t0) REVERT: D 105 VAL cc_start: 0.6545 (t) cc_final: 0.5889 (m) REVERT: F 86 ASP cc_start: 0.7684 (m-30) cc_final: 0.7176 (m-30) REVERT: G 33 VAL cc_start: 0.8948 (t) cc_final: 0.8671 (t) REVERT: G 65 SER cc_start: 0.8708 (p) cc_final: 0.8436 (m) outliers start: 75 outliers final: 54 residues processed: 330 average time/residue: 0.1288 time to fit residues: 69.6147 Evaluate side-chains 304 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 248 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain H residue 20 LEU 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 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 20 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 244 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 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 3 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 244 THR 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 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 105 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 45 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 GLN D 37 GLN D 38 HIS E 575 GLN G 38 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092263 restraints weight = 37314.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095128 restraints weight = 22058.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097044 restraints weight = 15716.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.098312 restraints weight = 12533.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099114 restraints weight = 10704.268| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4393 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= 0.155 Angle : 0.683 11.422 26952 Z= 0.339 Chirality : 0.044 0.260 3255 Planarity : 0.004 0.047 3273 Dihedral : 5.114 36.089 2485 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 3.45 % Allowed : 11.04 % 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: -0.93 (0.17), residues: 2286 helix: 0.94 (0.28), residues: 369 sheet: -0.44 (0.18), residues: 783 loop : -1.24 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 99 TYR 0.018 0.001 TYR G 67 PHE 0.014 0.002 PHE H 95 TRP 0.014 0.001 TRP F 62 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (19587) covalent geometry : angle 0.64579 / 0.33 (26622) SS BOND : bond 0.00532 / 0.37 ( 39) SS BOND : angle 1.47192 / 0.93 ( 78) hydrogen bonds : bond 0.04577 / 3.09 ( 679) hydrogen bonds : angle 5.62540 / 3.96 ( 1866) link_ALPHA1-2 : bond 0.00140 / 0.08 ( 6) link_ALPHA1-2 : angle 2.07030 / 1.28 ( 18) link_ALPHA1-3 : bond 0.00274 / 0.14 ( 6) link_ALPHA1-3 : angle 1.64604 / 1.05 ( 18) link_ALPHA1-6 : bond 0.00652 / 0.30 ( 3) link_ALPHA1-6 : angle 1.15151 / 0.60 ( 9) link_BETA1-4 : bond 0.00770 / 0.54 ( 24) link_BETA1-4 : angle 2.25296 / 1.55 ( 72) link_NAG-ASN : bond 0.00353 / 0.21 ( 45) link_NAG-ASN : angle 2.42828 / 1.76 ( 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 338 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7801 (tm-30) REVERT: A 478 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8241 (t0) REVERT: H 62 TRP cc_start: 0.7918 (p-90) cc_final: 0.7594 (p-90) REVERT: L 63 SER cc_start: 0.8972 (m) cc_final: 0.8580 (p) REVERT: L 65 SER cc_start: 0.8677 (p) cc_final: 0.8307 (m) REVERT: B 40 TYR cc_start: 0.8710 (t80) cc_final: 0.8408 (t80) REVERT: B 104 MET cc_start: 0.8819 (ttm) cc_final: 0.8546 (ttt) REVERT: B 323 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 482 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7491 (mm-30) REVERT: D 61 ARG cc_start: 0.7197 (mtp180) cc_final: 0.6904 (mtp85) REVERT: D 77 ASP cc_start: 0.6709 (t0) cc_final: 0.6378 (t0) REVERT: E 482 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7628 (mm-30) REVERT: E 651 ASN cc_start: 0.7486 (m-40) cc_final: 0.7138 (t0) REVERT: G 65 SER cc_start: 0.8644 (p) cc_final: 0.8398 (m) outliers start: 69 outliers final: 51 residues processed: 310 average time/residue: 0.1225 time to fit residues: 62.5249 Evaluate side-chains 300 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 244 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 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain H residue 20 LEU 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 3 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 131 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 51 ILE 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 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 255 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 424 ILE 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 3 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 196 optimal weight: 0.3980 chunk 172 optimal weight: 0.0030 chunk 65 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092932 restraints weight = 37325.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095729 restraints weight = 22822.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097614 restraints weight = 16533.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.098890 restraints weight = 13277.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099754 restraints weight = 11392.063| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19710 Z= 0.130 Angle : 0.655 12.214 26952 Z= 0.324 Chirality : 0.043 0.332 3255 Planarity : 0.004 0.049 3273 Dihedral : 4.943 34.754 2485 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.45 % Allowed : 11.34 % Favored : 85.21 % 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 (0.17), residues: 2286 helix: 1.12 (0.29), residues: 363 sheet: -0.33 (0.19), residues: 780 loop : -1.25 (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 A 522 TRP 0.017 0.001 TRP E 571 HIS 0.002 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19587) covalent geometry : angle 0.61974 / 0.32 (26622) SS BOND : bond 0.00550 / 0.35 ( 39) SS BOND : angle 1.38252 / 0.88 ( 78) hydrogen bonds : bond 0.04201 / 2.85 ( 679) hydrogen bonds : angle 5.47134 / 3.85 ( 1866) link_ALPHA1-2 : bond 0.00110 / 0.05 ( 6) link_ALPHA1-2 : angle 1.93481 / 1.20 ( 18) link_ALPHA1-3 : bond 0.00308 / 0.16 ( 6) link_ALPHA1-3 : angle 1.58870 / 1.01 ( 18) link_ALPHA1-6 : bond 0.00598 / 0.28 ( 3) link_ALPHA1-6 : angle 1.20955 / 0.63 ( 9) link_BETA1-4 : bond 0.00748 / 0.52 ( 24) link_BETA1-4 : angle 2.15129 / 1.48 ( 72) link_NAG-ASN : bond 0.00366 / 0.21 ( 45) link_NAG-ASN : angle 2.30779 / 1.68 ( 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 333 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 264 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7839 (tm-30) REVERT: A 478 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (t0) REVERT: A 651 ASN cc_start: 0.7555 (OUTLIER) cc_final: 0.7070 (t0) REVERT: H 62 TRP cc_start: 0.7927 (p-90) cc_final: 0.7569 (p-90) REVERT: L 63 SER cc_start: 0.8948 (m) cc_final: 0.8584 (p) REVERT: L 65 SER cc_start: 0.8607 (p) cc_final: 0.8242 (m) REVERT: B 104 MET cc_start: 0.8818 (ttm) cc_final: 0.8536 (ttt) REVERT: B 323 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8904 (tt) REVERT: B 482 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 619 LEU cc_start: 0.7495 (mt) cc_final: 0.7227 (mm) REVERT: C 35 MET cc_start: 0.7340 (mmm) cc_final: 0.7135 (mmm) REVERT: D 77 ASP cc_start: 0.6800 (t0) cc_final: 0.6581 (t0) REVERT: E 447 SER cc_start: 0.9240 (m) cc_final: 0.9031 (m) REVERT: E 482 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7484 (mm-30) REVERT: E 651 ASN cc_start: 0.7427 (m-40) cc_final: 0.7188 (t0) REVERT: F 86 ASP cc_start: 0.7565 (m-30) cc_final: 0.7131 (m-30) REVERT: G 65 SER cc_start: 0.8530 (p) cc_final: 0.8231 (m) REVERT: G 105 VAL cc_start: 0.6749 (t) cc_final: 0.5580 (m) outliers start: 69 outliers final: 50 residues processed: 311 average time/residue: 0.1174 time to fit residues: 61.0331 Evaluate side-chains 294 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 VAL 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 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 543 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER 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 49 ILE 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 323 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 51 ILE 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 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 371 VAL 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 108 LEU 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 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 124 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 101 optimal weight: 0.0570 chunk 194 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN G 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.090757 restraints weight = 37647.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.093531 restraints weight = 23017.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095408 restraints weight = 16654.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096669 restraints weight = 13385.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097454 restraints weight = 11502.305| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4707 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= 0.183 Angle : 0.692 9.654 26952 Z= 0.342 Chirality : 0.045 0.508 3255 Planarity : 0.004 0.050 3273 Dihedral : 4.970 34.600 2485 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.35 % Allowed : 11.29 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.17), residues: 2286 helix: 1.08 (0.29), residues: 363 sheet: -0.36 (0.19), residues: 780 loop : -1.32 (0.17), residues: 1143 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 0.017 0.002 PHE H 95 TRP 0.017 0.001 TRP E 571 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 (19587) covalent geometry : angle 0.65466 / 0.33 (26622) SS BOND : bond 0.00546 / 0.35 ( 39) SS BOND : angle 1.57297 / 0.99 ( 78) hydrogen bonds : bond 0.04473 / 3.04 ( 679) hydrogen bonds : angle 5.53706 / 3.90 ( 1866) link_ALPHA1-2 : bond 0.00167 / 0.08 ( 6) link_ALPHA1-2 : angle 2.21879 / 1.39 ( 18) link_ALPHA1-3 : bond 0.00240 / 0.13 ( 6) link_ALPHA1-3 : angle 1.66113 / 1.08 ( 18) link_ALPHA1-6 : bond 0.00633 / 0.29 ( 3) link_ALPHA1-6 : angle 1.16643 / 0.61 ( 9) link_BETA1-4 : bond 0.00674 / 0.47 ( 24) link_BETA1-4 : angle 2.28335 / 1.57 ( 72) link_NAG-ASN : bond 0.00363 / 0.21 ( 45) link_NAG-ASN : angle 2.41139 / 1.72 ( 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 321 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8145 (tm-30) cc_final: 0.7904 (tm-30) REVERT: A 478 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8300 (t0) REVERT: H 2 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7293 (mp10) REVERT: H 62 TRP cc_start: 0.7993 (p-90) cc_final: 0.7612 (p-90) REVERT: L 63 SER cc_start: 0.9017 (m) cc_final: 0.8669 (p) REVERT: L 65 SER cc_start: 0.8619 (p) cc_final: 0.8235 (m) REVERT: B 104 MET cc_start: 0.8863 (ttm) cc_final: 0.8605 (ttt) REVERT: B 323 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 482 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 651 ASN cc_start: 0.7406 (OUTLIER) cc_final: 0.6988 (t0) REVERT: C 81 MET cc_start: 0.6763 (mtm) cc_final: 0.6488 (mtt) REVERT: E 482 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7520 (mm-30) REVERT: F 2 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7137 (mp10) REVERT: G 65 SER cc_start: 0.8510 (p) cc_final: 0.8197 (m) outliers start: 67 outliers final: 56 residues processed: 299 average time/residue: 0.1157 time to fit residues: 58.6577 Evaluate side-chains 298 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 239 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU 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 543 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER 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 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 651 ASN Chi-restraints excluded: chain C residue 7 SER 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 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 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 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 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 47 LEU Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 0.0470 chunk 194 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 208 optimal weight: 0.2980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN H 66 GLN L 37 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN E 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.092859 restraints weight = 37531.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095660 restraints weight = 22804.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.097525 restraints weight = 16497.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098797 restraints weight = 13263.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.099660 restraints weight = 11378.620| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19710 Z= 0.128 Angle : 0.649 13.252 26952 Z= 0.322 Chirality : 0.043 0.390 3255 Planarity : 0.004 0.048 3273 Dihedral : 4.873 34.057 2485 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.90 % Allowed : 12.19 % Favored : 84.91 % 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: -0.85 (0.17), residues: 2286 helix: 1.18 (0.29), residues: 363 sheet: -0.28 (0.19), residues: 792 loop : -1.36 (0.17), residues: 1131 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 0.012 0.001 PHE H 95 TRP 0.016 0.001 TRP F 62 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (19587) covalent geometry : angle 0.61365 / 0.31 (26622) SS BOND : bond 0.00709 / 0.52 ( 39) SS BOND : angle 1.52984 / 0.98 ( 78) hydrogen bonds : bond 0.04092 / 2.77 ( 679) hydrogen bonds : angle 5.42191 / 3.82 ( 1866) link_ALPHA1-2 : bond 0.00189 / 0.08 ( 6) link_ALPHA1-2 : angle 1.90156 / 1.16 ( 18) link_ALPHA1-3 : bond 0.00338 / 0.17 ( 6) link_ALPHA1-3 : angle 1.57598 / 1.00 ( 18) link_ALPHA1-6 : bond 0.00562 / 0.26 ( 3) link_ALPHA1-6 : angle 1.24629 / 0.65 ( 9) link_BETA1-4 : bond 0.00765 / 0.53 ( 24) link_BETA1-4 : angle 2.12653 / 1.46 ( 72) link_NAG-ASN : bond 0.00308 / 0.18 ( 45) link_NAG-ASN : angle 2.24382 / 1.63 ( 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 309 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7830 (tm-30) REVERT: A 478 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (t0) REVERT: H 62 TRP cc_start: 0.8013 (p-90) cc_final: 0.7638 (p-90) REVERT: L 63 SER cc_start: 0.8988 (m) cc_final: 0.8643 (p) REVERT: L 65 SER cc_start: 0.8601 (p) cc_final: 0.8175 (m) REVERT: B 104 MET cc_start: 0.8820 (ttm) cc_final: 0.8542 (ttt) REVERT: B 323 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8955 (tt) REVERT: B 482 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7372 (mm-30) REVERT: B 650 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: C 2 GLN cc_start: 0.7828 (mm-40) cc_final: 0.7445 (mp10) REVERT: D 42 GLN cc_start: 0.7842 (mp10) cc_final: 0.7611 (pm20) REVERT: E 482 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7430 (mm-30) REVERT: E 651 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6902 (t0) REVERT: F 2 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7269 (mp10) REVERT: F 86 ASP cc_start: 0.7640 (m-30) cc_final: 0.7219 (m-30) REVERT: G 33 VAL cc_start: 0.8786 (t) cc_final: 0.8582 (t) REVERT: G 65 SER cc_start: 0.8493 (p) cc_final: 0.8177 (m) REVERT: G 105 VAL cc_start: 0.6755 (t) cc_final: 0.5774 (m) outliers start: 58 outliers final: 41 residues processed: 293 average time/residue: 0.1122 time to fit residues: 55.6697 Evaluate side-chains 279 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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 150 MET Chi-restraints excluded: chain A residue 255 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 H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE 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 49 ILE 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 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 650 GLN 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 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 540 GLN Chi-restraints excluded: chain E residue 651 ASN 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 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: 5.9990 chunk 157 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 4 optimal weight: 0.0270 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN L 38 HIS ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN B 651 ASN E 651 ASN F 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090943 restraints weight = 37463.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.093634 restraints weight = 22944.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095495 restraints weight = 16741.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096741 restraints weight = 13461.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.097585 restraints weight = 11578.054| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19710 Z= 0.176 Angle : 0.695 14.081 26952 Z= 0.345 Chirality : 0.044 0.312 3255 Planarity : 0.004 0.050 3273 Dihedral : 4.893 33.808 2485 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.70 % Allowed : 12.89 % 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: -0.96 (0.17), residues: 2286 helix: 1.11 (0.29), residues: 363 sheet: -0.34 (0.19), residues: 780 loop : -1.42 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 298 TYR 0.023 0.001 TYR G 67 PHE 0.017 0.002 PHE H 95 TRP 0.039 0.001 TRP B 571 HIS 0.002 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (19587) covalent geometry : angle 0.66046 / 0.34 (26622) SS BOND : bond 0.00524 / 0.33 ( 39) SS BOND : angle 1.52943 / 0.96 ( 78) hydrogen bonds : bond 0.04328 / 2.94 ( 679) hydrogen bonds : angle 5.50395 / 3.88 ( 1866) link_ALPHA1-2 : bond 0.00136 / 0.07 ( 6) link_ALPHA1-2 : angle 2.21393 / 1.38 ( 18) link_ALPHA1-3 : bond 0.00263 / 0.14 ( 6) link_ALPHA1-3 : angle 1.62940 / 1.06 ( 18) link_ALPHA1-6 : bond 0.00619 / 0.29 ( 3) link_ALPHA1-6 : angle 1.19842 / 0.63 ( 9) link_BETA1-4 : bond 0.00686 / 0.48 ( 24) link_BETA1-4 : angle 2.24577 / 1.55 ( 72) link_NAG-ASN : bond 0.00314 / 0.19 ( 45) link_NAG-ASN : angle 2.31983 / 1.69 ( 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 300 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 246 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7865 (tm-30) REVERT: A 478 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8304 (t0) REVERT: H 2 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7384 (mp10) REVERT: H 62 TRP cc_start: 0.7989 (p-90) cc_final: 0.7571 (p-90) REVERT: L 63 SER cc_start: 0.9029 (m) cc_final: 0.8676 (p) REVERT: L 65 SER cc_start: 0.8667 (p) cc_final: 0.8217 (m) REVERT: B 104 MET cc_start: 0.8844 (ttm) cc_final: 0.8588 (ttt) REVERT: B 323 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 482 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7394 (mm-30) REVERT: B 650 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6954 (mp10) REVERT: C 2 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7370 (mp10) REVERT: E 482 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7423 (mm-30) REVERT: F 2 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7290 (mp10) REVERT: G 33 VAL cc_start: 0.8840 (t) cc_final: 0.8638 (t) REVERT: G 65 SER cc_start: 0.8443 (p) cc_final: 0.8066 (m) REVERT: G 105 VAL cc_start: 0.6328 (t) cc_final: 0.5839 (m) outliers start: 54 outliers final: 44 residues processed: 285 average time/residue: 0.1144 time to fit residues: 54.6461 Evaluate side-chains 286 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 239 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 255 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 543 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 SER 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 49 ILE 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 162 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 323 ILE 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 650 GLN 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 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 461 THR 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 20 THR Chi-restraints excluded: chain G residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 101 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 0.0770 chunk 65 optimal weight: 1.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 651 ASN B 72 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.093192 restraints weight = 37514.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.096002 restraints weight = 22653.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.097899 restraints weight = 16297.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.099175 restraints weight = 13060.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099967 restraints weight = 11190.061| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19710 Z= 0.128 Angle : 0.653 13.065 26952 Z= 0.325 Chirality : 0.043 0.302 3255 Planarity : 0.004 0.049 3273 Dihedral : 4.816 33.322 2485 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.15 % Allowed : 13.59 % Favored : 84.26 % 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: -0.87 (0.18), residues: 2286 helix: 1.16 (0.29), residues: 363 sheet: -0.17 (0.19), residues: 789 loop : -1.47 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 28 TYR 0.020 0.001 TYR G 67 PHE 0.014 0.001 PHE H 95 TRP 0.050 0.001 TRP B 571 HIS 0.002 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (19587) covalent geometry : angle 0.61976 / 0.32 (26622) SS BOND : bond 0.00516 / 0.33 ( 39) SS BOND : angle 1.47850 / 0.93 ( 78) hydrogen bonds : bond 0.03960 / 2.68 ( 679) hydrogen bonds : angle 5.40617 / 3.81 ( 1866) link_ALPHA1-2 : bond 0.00216 / 0.09 ( 6) link_ALPHA1-2 : angle 1.87293 / 1.14 ( 18) link_ALPHA1-3 : bond 0.00348 / 0.18 ( 6) link_ALPHA1-3 : angle 1.55953 / 0.99 ( 18) link_ALPHA1-6 : bond 0.00568 / 0.26 ( 3) link_ALPHA1-6 : angle 1.25893 / 0.66 ( 9) link_BETA1-4 : bond 0.00762 / 0.53 ( 24) link_BETA1-4 : angle 2.11651 / 1.45 ( 72) link_NAG-ASN : bond 0.00303 / 0.18 ( 45) link_NAG-ASN : angle 2.19824 / 1.61 ( 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 290 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 478 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8253 (t0) REVERT: H 2 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7389 (mp10) REVERT: H 62 TRP cc_start: 0.7998 (p-90) cc_final: 0.7576 (p-90) REVERT: L 63 SER cc_start: 0.8970 (m) cc_final: 0.8639 (p) REVERT: B 104 MET cc_start: 0.8819 (ttm) cc_final: 0.8544 (ttt) REVERT: B 246 GLN cc_start: 0.6859 (pm20) cc_final: 0.6225 (tt0) REVERT: B 323 ILE cc_start: 0.9219 (mt) cc_final: 0.8996 (tt) REVERT: B 482 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 2 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7373 (mp10) REVERT: C 35 MET cc_start: 0.7429 (tpp) cc_final: 0.7166 (mmm) REVERT: E 482 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7396 (mm-30) REVERT: E 494 LEU cc_start: 0.8813 (mt) cc_final: 0.8586 (tp) REVERT: F 2 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7300 (mp10) outliers start: 43 outliers final: 36 residues processed: 279 average time/residue: 0.1171 time to fit residues: 55.1815 Evaluate side-chains 274 residues out of total 2001 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 447 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 73 SER 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 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 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 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 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 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 chunk 175 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 651 ASN B 72 HIS B 279 ASN B 650 GLN E 88 ASN E 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.115747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.093586 restraints weight = 37397.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096420 restraints weight = 22732.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098318 restraints weight = 16333.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099601 restraints weight = 13075.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100394 restraints weight = 11201.713| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19710 Z= 0.123 Angle : 0.639 12.595 26952 Z= 0.319 Chirality : 0.043 0.271 3255 Planarity : 0.004 0.050 3273 Dihedral : 4.759 32.900 2485 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.30 % Allowed : 13.74 % Favored : 83.96 % 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: -0.82 (0.18), residues: 2286 helix: 1.22 (0.29), residues: 363 sheet: -0.13 (0.19), residues: 789 loop : -1.45 (0.17), residues: 1134 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 0.014 0.001 PHE H 95 TRP 0.040 0.001 TRP B 571 HIS 0.002 0.001 HIS G 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (19587) covalent geometry : angle 0.60647 / 0.31 (26622) SS BOND : bond 0.00489 / 0.31 ( 39) SS BOND : angle 1.41805 / 0.89 ( 78) hydrogen bonds : bond 0.03830 / 2.59 ( 679) hydrogen bonds : angle 5.35343 / 3.77 ( 1866) link_ALPHA1-2 : bond 0.00227 / 0.10 ( 6) link_ALPHA1-2 : angle 1.90800 / 1.17 ( 18) link_ALPHA1-3 : bond 0.00356 / 0.18 ( 6) link_ALPHA1-3 : angle 1.51631 / 0.96 ( 18) link_ALPHA1-6 : bond 0.00561 / 0.26 ( 3) link_ALPHA1-6 : angle 1.26840 / 0.67 ( 9) link_BETA1-4 : bond 0.00704 / 0.49 ( 24) link_BETA1-4 : angle 2.09644 / 1.44 ( 72) link_NAG-ASN : bond 0.00288 / 0.17 ( 45) link_NAG-ASN : angle 2.12957 / 1.57 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3122.29 seconds wall clock time: 55 minutes 3.64 seconds (3303.64 seconds total)