Starting phenix.real_space_refine on Thu Aug 6 16:10:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.map" model { file = "/net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pyh_72033/08_2026/9pyh_72033.cif" } resolution = 3.3 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= 0.006 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 108 5.16 5 C 9778 2.51 5 N 2616 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15624 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4337 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 6 Chain: "B" Number of atoms: 4157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4157 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 22, 'TRANS': 504} Chain breaks: 8 Chain: "C" Number of atoms: 4313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4313 Classifications: {'peptide': 546} Link IDs: {'PTRANS': 23, 'TRANS': 522} Chain breaks: 6 Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1019 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.48, per 1000 atoms: 0.22 Number of scatterers: 15624 At special positions: 0 Unit cell: (121.342, 126.368, 150.78, 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 108 16.00 O 3122 8.00 N 2616 7.00 C 9778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 119 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.11 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 T 4 " - " MAN T 5 " ALPHA1-3 " BMA T 3 " - " MAN T 4 " ALPHA1-6 " BMA K 3 " - " MAN K 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " 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 M 2 " - " BMA M 3 " " 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 R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 701 " - " ASN A 133 " " NAG A 702 " - " ASN A 234 " " NAG A 703 " - " ASN A 295 " " NAG A 704 " - " ASN A 301 " " NAG A 705 " - " ASN A 339 " " NAG A 706 " - " ASN A 448 " " NAG A 707 " - " ASN A 355 " " NAG A 708 " - " ASN A 392 " " NAG A 709 " - " ASN A 363 " " NAG B 701 " - " ASN B 88 " " NAG B 702 " - " ASN B 133 " " NAG B 703 " - " ASN B 156 " " NAG B 704 " - " ASN B 197 " " NAG B 705 " - " ASN B 234 " " NAG B 706 " - " ASN B 276 " " NAG B 707 " - " ASN B 301 " " NAG B 708 " - " ASN B 339 " " NAG B 709 " - " ASN B 363 " " NAG B 710 " - " ASN B 392 " " NAG C 701 " - " ASN C 88 " " NAG C 702 " - " ASN C 197 " " NAG C 703 " - " ASN C 234 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 301 " " NAG C 706 " - " ASN C 339 " " NAG C 707 " - " ASN C 355 " " NAG C 708 " - " ASN C 386 " " NAG C 709 " - " ASN C 392 " " NAG C 710 " - " ASN C 448 " " NAG C 711 " - " ASN C 276 " " NAG D 1 " - " ASN A 156 " " NAG E 1 " - " ASN A 160 " " NAG F 1 " - " ASN A 197 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN A 332 " " NAG J 1 " - " ASN A 386 " " NAG K 1 " - " ASN B 160 " " NAG M 1 " - " ASN B 262 " " NAG N 1 " - " ASN B 332 " " NAG O 1 " - " ASN B 295 " " NAG P 1 " - " ASN B 386 " " NAG Q 1 " - " ASN B 448 " " NAG R 1 " - " ASN C 133 " " NAG S 1 " - " ASN C 156 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 262 " " NAG V 1 " - " ASN C 332 " Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3462 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 31 sheets defined 22.4% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.152A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.793A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.946A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.890A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 3.832A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 535 removed outlier: 4.217A pdb=" N MET A 535 " --> pdb=" O ALA A 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 532 through 535' Processing helix chain 'A' and resid 536 through 541 removed outlier: 4.006A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 596 Processing helix chain 'A' and resid 618 through 626 removed outlier: 3.924A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 648 removed outlier: 3.854A pdb=" N ILE A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 662 removed outlier: 3.700A pdb=" N CYS A 662 " --> pdb=" O GLN A 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.170A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.720A pdb=" N HIS B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.921A pdb=" N THR B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 4.179A pdb=" N GLN B 428 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG B 429 " --> pdb=" O MET B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 429' Processing helix chain 'B' and resid 475 through 481 removed outlier: 4.142A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 536 removed outlier: 3.580A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'C' and resid 94 through 97 removed outlier: 3.640A pdb=" N LYS C 97 " --> pdb=" O ASN C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.114A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 3.678A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.649A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.606A pdb=" N THR C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 3.814A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 543 removed outlier: 3.854A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 595 Processing helix chain 'C' and resid 618 through 625 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 650 removed outlier: 3.599A pdb=" N GLN C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 656 removed outlier: 3.657A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.772A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.755A 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 removed outlier: 3.642A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) 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 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.289A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.795A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.371A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 497 Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 47 removed outlier: 4.481A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'B' and resid 129 through 133 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 168 through 177 current: chain 'B' and resid 189 through 193 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 189 through 193 current: chain 'H' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB5, first strand: chain 'B' and resid 200 through 203 removed outlier: 5.967A pdb=" N ALA B 200 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR B 435 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 259 through 260 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 260 current: chain 'B' and resid 284 through 298 removed outlier: 6.144A pdb=" N GLN B 293 " --> pdb=" O SER B 334 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 332 through 334 current: chain 'B' and resid 393 through 395 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 393 through 395 current: chain 'B' and resid 466 through 470 Processing sheet with id=AB7, first strand: chain 'B' and resid 302 through 312 removed outlier: 6.364A pdb=" N THR B 303 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 374 through 378 removed outlier: 4.106A pdb=" N PHE B 382 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 495 through 497 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 Processing sheet with id=AC4, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.445A pdb=" N ILE C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC7, first strand: chain 'C' and resid 260 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 260 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.110A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 329 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 466 through 470 Processing sheet with id=AC8, first strand: chain 'C' and resid 301 through 312 removed outlier: 4.320A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS C 305 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N MET C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.765A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.959A pdb=" N ASP L 70 " --> pdb=" O TYR L 67 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.811A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.753A pdb=" N SER L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1302 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: 2.63 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 5050 1.37 - 1.52: 6243 1.52 - 1.67: 4480 1.67 - 1.82: 142 1.82 - 1.97: 6 Bond restraints: 15921 Sorted by residual: bond pdb=" CB CYS B 445 " pdb=" SG CYS B 445 " ideal model delta sigma weight residual 1.808 1.974 -0.166 3.30e-02 9.18e+02 2.54e+01 bond pdb=" CB CYS B 331 " pdb=" SG CYS B 331 " ideal model delta sigma weight residual 1.808 1.932 -0.124 3.30e-02 9.18e+02 1.40e+01 bond pdb=" N PHE B 376 " pdb=" CA PHE B 376 " ideal model delta sigma weight residual 1.455 1.488 -0.034 1.27e-02 6.20e+03 6.98e+00 bond pdb=" N CYS B 378 " pdb=" CA CYS B 378 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.57e+00 bond pdb=" CB CYS B 296 " pdb=" SG CYS B 296 " ideal model delta sigma weight residual 1.808 1.726 0.082 3.30e-02 9.18e+02 6.18e+00 ... (remaining 15916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 21504 4.29 - 8.59: 87 8.59 - 12.88: 6 12.88 - 17.18: 2 17.18 - 21.47: 1 Bond angle restraints: 21600 Sorted by residual: angle pdb=" CA CYS B 445 " pdb=" CB CYS B 445 " pdb=" SG CYS B 445 " ideal model delta sigma weight residual 114.40 135.87 -21.47 2.30e+00 1.89e-01 8.72e+01 angle pdb=" C CYS B 331 " pdb=" CA CYS B 331 " pdb=" CB CYS B 331 " ideal model delta sigma weight residual 109.89 119.41 -9.52 1.60e+00 3.91e-01 3.54e+01 angle pdb=" C2 NAG V 1 " pdb=" N2 NAG V 1 " pdb=" C7 NAG V 1 " ideal model delta sigma weight residual 124.56 140.91 -16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C ASN B 332 " pdb=" CA ASN B 332 " pdb=" CB ASN B 332 " ideal model delta sigma weight residual 110.19 102.81 7.38 1.64e+00 3.72e-01 2.03e+01 angle pdb=" N HIS B 374 " pdb=" CA HIS B 374 " pdb=" C HIS B 374 " ideal model delta sigma weight residual 110.80 101.63 9.17 2.13e+00 2.20e-01 1.85e+01 ... (remaining 21595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 10055 19.03 - 38.06: 346 38.06 - 57.09: 90 57.09 - 76.13: 27 76.13 - 95.16: 10 Dihedral angle restraints: 10528 sinusoidal: 5176 harmonic: 5352 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 161.56 -68.56 1 1.00e+01 1.00e-02 6.09e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -37.85 -48.15 1 1.00e+01 1.00e-02 3.20e+01 dihedral pdb=" CB CYS B 119 " pdb=" SG CYS B 119 " pdb=" SG CYS B 205 " pdb=" CB CYS B 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.21 43.21 1 1.00e+01 1.00e-02 2.60e+01 ... (remaining 10525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 2375 0.097 - 0.194: 254 0.194 - 0.290: 12 0.290 - 0.387: 2 0.387 - 0.484: 1 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE B 294 " pdb=" CA ILE B 294 " pdb=" CG1 ILE B 294 " pdb=" CG2 ILE B 294 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C1 NAG C 702 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 702 " pdb=" O5 NAG C 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 294 " pdb=" CA ILE A 294 " pdb=" CG1 ILE A 294 " pdb=" CG2 ILE A 294 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 2641 not shown) Planarity restraints: 2700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 296 " 0.020 2.00e-02 2.50e+03 4.22e-02 1.78e+01 pdb=" C CYS B 296 " -0.073 2.00e-02 2.50e+03 pdb=" O CYS B 296 " 0.028 2.00e-02 2.50e+03 pdb=" N THR B 297 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 36 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C TYR L 36 " -0.060 2.00e-02 2.50e+03 pdb=" O TYR L 36 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN L 37 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 385 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C CYS B 385 " -0.046 2.00e-02 2.50e+03 pdb=" O CYS B 385 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN B 386 " 0.015 2.00e-02 2.50e+03 ... (remaining 2697 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 6896 2.97 - 3.45: 14488 3.45 - 3.94: 25515 3.94 - 4.42: 27975 4.42 - 4.90: 48088 Nonbonded interactions: 122962 Sorted by model distance: nonbonded pdb=" O5 NAG J 1 " pdb=" O6 NAG J 1 " model vdw 2.492 2.432 nonbonded pdb=" O2 BMA K 3 " pdb=" O3 BMA K 3 " model vdw 2.547 2.432 nonbonded pdb=" O5 MAN T 4 " pdb=" O6 MAN T 4 " model vdw 2.559 2.432 nonbonded pdb=" N CYS B 296 " pdb=" O CYS B 445 " model vdw 2.575 3.120 nonbonded pdb=" O2 BMA J 3 " pdb=" O3 BMA J 3 " model vdw 2.599 2.432 ... (remaining 122957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 36 through 56 or resid 73 through 77 or resid 81 through 1 \ 35 or resid 150 through 501 or resid 522 through 569 or resid 573 through 657 or \ resid 701 through 709)) selection = (chain 'B' and (resid 36 through 185 or resid 189 through 398 or resid 412 throu \ gh 457 or resid 465 through 501 or resid 522 through 657 or resid 702 through 71 \ 0)) selection = (chain 'C' and (resid 36 through 56 or resid 73 through 77 or resid 81 through 1 \ 35 or resid 150 through 185 or resid 189 through 464 or resid 466 through 501 or \ resid 522 through 546 or resid 569 or resid 573 through 657 or resid 703 throug \ h 711)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'V' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'U' } 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 individual isotropic 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: 8.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.330 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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 : 0.005 0.166 16027 Z= 0.245 Angle : 0.913 21.473 21885 Z= 0.474 Chirality : 0.057 0.484 2644 Planarity : 0.007 0.078 2653 Dihedral : 10.848 95.157 6967 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.17 (0.19), residues: 1807 helix: 0.74 (0.28), residues: 370 sheet: -0.86 (0.21), residues: 545 loop : -1.33 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 298 TYR 0.024 0.002 TYR L 91 PHE 0.031 0.002 PHE H 78 TRP 0.021 0.002 TRP B 479 HIS 0.007 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (15921) covalent geometry : angle 0.87926 / 0.47 (21600) SS BOND : bond 0.01496 / 1.11 ( 33) SS BOND : angle 1.86228 / 1.11 ( 66) hydrogen bonds : bond 0.11332 / 7.29 ( 475) hydrogen bonds : angle 6.39757 / 4.50 ( 1302) link_ALPHA1-2 : bond 0.00367 / 0.19 ( 1) link_ALPHA1-2 : angle 3.06068 / 1.62 ( 3) link_ALPHA1-3 : bond 0.01289 / 0.68 ( 1) link_ALPHA1-3 : angle 1.20893 / 0.64 ( 3) link_ALPHA1-6 : bond 0.00710 / 0.37 ( 1) link_ALPHA1-6 : angle 1.27345 / 0.71 ( 3) link_BETA1-4 : bond 0.00846 / 0.47 ( 23) link_BETA1-4 : angle 2.09750 / 1.55 ( 69) link_NAG-ASN : bond 0.00562 / 0.34 ( 47) link_NAG-ASN : angle 2.64495 / 2.00 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6873 (pt0) REVERT: A 136 ASN cc_start: 0.7822 (t0) cc_final: 0.7606 (t0) REVERT: A 356 ASN cc_start: 0.8315 (p0) cc_final: 0.7854 (p0) REVERT: B 46 LYS cc_start: 0.8110 (mttp) cc_final: 0.7891 (mtmt) REVERT: B 151 ARG cc_start: 0.7650 (tpt90) cc_final: 0.7271 (mtm-85) REVERT: B 161 MET cc_start: 0.8659 (tpp) cc_final: 0.8166 (tpp) REVERT: B 189 LYS cc_start: 0.8349 (mttt) cc_final: 0.8088 (mttm) REVERT: B 318 TYR cc_start: 0.8794 (m-80) cc_final: 0.8434 (m-80) REVERT: B 326 ILE cc_start: 0.8350 (mt) cc_final: 0.8113 (tt) REVERT: B 543 ASN cc_start: 0.7963 (m-40) cc_final: 0.7507 (m110) REVERT: B 607 ASN cc_start: 0.7106 (m-40) cc_final: 0.6182 (p0) REVERT: B 645 LEU cc_start: 0.7519 (mt) cc_final: 0.7136 (mp) REVERT: C 49 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7702 (mm-30) REVERT: C 211 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8035 (tp30) REVERT: C 303 THR cc_start: 0.7538 (m) cc_final: 0.7091 (p) REVERT: C 318 TYR cc_start: 0.8757 (m-80) cc_final: 0.8443 (m-80) REVERT: C 322 ASP cc_start: 0.7202 (t0) cc_final: 0.6820 (t0) REVERT: C 632 ASP cc_start: 0.8555 (t70) cc_final: 0.8321 (t0) REVERT: H 28 PHE cc_start: 0.7616 (m-80) cc_final: 0.6749 (t80) REVERT: H 79 SER cc_start: 0.8448 (p) cc_final: 0.8172 (m) REVERT: H 82 ILE cc_start: 0.8792 (mm) cc_final: 0.8510 (mt) REVERT: H 82 SER cc_start: 0.8967 (m) cc_final: 0.8685 (p) REVERT: L 93 SER cc_start: 0.8369 (p) cc_final: 0.8026 (m) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1201 time to fit residues: 69.0543 Evaluate side-chains 219 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN B 82 GLN B 85 HIS B 195 ASN B 651 ASN C 103 GLN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.152830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125456 restraints weight = 18982.845| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.74 r_work: 0.3210 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16027 Z= 0.152 Angle : 0.630 10.001 21885 Z= 0.309 Chirality : 0.047 0.363 2644 Planarity : 0.005 0.061 2653 Dihedral : 6.453 92.782 3490 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.65 % Allowed : 7.20 % Favored : 91.15 % 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: -0.89 (0.20), residues: 1807 helix: 1.11 (0.28), residues: 370 sheet: -0.72 (0.21), residues: 552 loop : -1.21 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 81 TYR 0.022 0.001 TYR B 217 PHE 0.022 0.002 PHE H 78 TRP 0.015 0.001 TRP A 96 HIS 0.004 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (15921) covalent geometry : angle 0.58988 / 0.30 (21600) SS BOND : bond 0.00292 / 0.20 ( 33) SS BOND : angle 1.54474 / 1.13 ( 66) hydrogen bonds : bond 0.03715 / 2.50 ( 475) hydrogen bonds : angle 5.22188 / 3.71 ( 1302) link_ALPHA1-2 : bond 0.00288 / 0.15 ( 1) link_ALPHA1-2 : angle 2.69538 / 1.45 ( 3) link_ALPHA1-3 : bond 0.00971 / 0.51 ( 1) link_ALPHA1-3 : angle 1.08141 / 0.60 ( 3) link_ALPHA1-6 : bond 0.00962 / 0.51 ( 1) link_ALPHA1-6 : angle 1.47716 / 0.82 ( 3) link_BETA1-4 : bond 0.00422 / 0.25 ( 23) link_BETA1-4 : angle 1.59073 / 1.17 ( 69) link_NAG-ASN : bond 0.00381 / 0.17 ( 47) link_NAG-ASN : angle 2.38342 / 1.75 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6937 (pt0) REVERT: A 136 ASN cc_start: 0.7813 (t0) cc_final: 0.7511 (t0) REVERT: B 46 LYS cc_start: 0.8193 (mttp) cc_final: 0.7981 (mtmt) REVERT: B 151 ARG cc_start: 0.7789 (tpt90) cc_final: 0.7232 (mtm-85) REVERT: B 318 TYR cc_start: 0.8978 (m-80) cc_final: 0.8580 (m-80) REVERT: B 444 ARG cc_start: 0.8386 (tmt170) cc_final: 0.8153 (mtp-110) REVERT: B 543 ASN cc_start: 0.8031 (m-40) cc_final: 0.7530 (m110) REVERT: B 544 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7771 (mp) REVERT: B 607 ASN cc_start: 0.7047 (m-40) cc_final: 0.6198 (p0) REVERT: B 631 TRP cc_start: 0.8033 (t-100) cc_final: 0.7804 (t-100) REVERT: C 39 TYR cc_start: 0.8644 (m-80) cc_final: 0.8426 (m-80) REVERT: C 49 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7765 (mm-30) REVERT: C 232 LYS cc_start: 0.8045 (pttp) cc_final: 0.7711 (ptpt) REVERT: C 280 ASN cc_start: 0.7875 (m-40) cc_final: 0.7214 (t0) REVERT: C 303 THR cc_start: 0.7659 (m) cc_final: 0.7161 (p) REVERT: C 318 TYR cc_start: 0.8883 (m-80) cc_final: 0.8608 (m-80) REVERT: C 322 ASP cc_start: 0.7564 (t0) cc_final: 0.7025 (t0) REVERT: C 584 GLU cc_start: 0.8192 (tt0) cc_final: 0.7921 (tt0) REVERT: C 632 ASP cc_start: 0.8807 (t70) cc_final: 0.8566 (t0) REVERT: H 28 PHE cc_start: 0.7791 (m-80) cc_final: 0.6711 (t80) REVERT: H 79 SER cc_start: 0.8612 (p) cc_final: 0.8257 (m) REVERT: H 82 ILE cc_start: 0.8804 (mm) cc_final: 0.8525 (mt) REVERT: H 82 SER cc_start: 0.9024 (m) cc_final: 0.8616 (p) REVERT: L 93 SER cc_start: 0.8629 (p) cc_final: 0.8248 (m) outliers start: 27 outliers final: 17 residues processed: 254 average time/residue: 0.1138 time to fit residues: 44.8793 Evaluate side-chains 227 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 179 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 ASN B 425 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119190 restraints weight = 19323.712| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.75 r_work: 0.3124 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16027 Z= 0.216 Angle : 0.665 11.554 21885 Z= 0.326 Chirality : 0.049 0.353 2644 Planarity : 0.004 0.049 2653 Dihedral : 6.626 96.610 3490 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.50 % Allowed : 8.73 % Favored : 88.77 % 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 (0.20), residues: 1807 helix: 1.11 (0.28), residues: 370 sheet: -0.91 (0.21), residues: 560 loop : -1.17 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 298 TYR 0.021 0.002 TYR L 91 PHE 0.025 0.002 PHE H 78 TRP 0.016 0.002 TRP B 479 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.22 (15921) covalent geometry : angle 0.62948 / 0.32 (21600) SS BOND : bond 0.00422 / 0.29 ( 33) SS BOND : angle 1.59180 / 1.12 ( 66) hydrogen bonds : bond 0.03909 / 2.64 ( 475) hydrogen bonds : angle 5.20101 / 3.67 ( 1302) link_ALPHA1-2 : bond 0.00447 / 0.24 ( 1) link_ALPHA1-2 : angle 2.77479 / 1.49 ( 3) link_ALPHA1-3 : bond 0.01096 / 0.58 ( 1) link_ALPHA1-3 : angle 1.05052 / 0.58 ( 3) link_ALPHA1-6 : bond 0.01185 / 0.62 ( 1) link_ALPHA1-6 : angle 1.69874 / 0.93 ( 3) link_BETA1-4 : bond 0.00509 / 0.28 ( 23) link_BETA1-4 : angle 1.69319 / 1.21 ( 69) link_NAG-ASN : bond 0.00420 / 0.24 ( 47) link_NAG-ASN : angle 2.25235 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7111 (pt0) REVERT: A 83 GLU cc_start: 0.8009 (pt0) cc_final: 0.7786 (pt0) REVERT: A 136 ASN cc_start: 0.7903 (t0) cc_final: 0.7581 (t0) REVERT: A 158 SER cc_start: 0.8805 (m) cc_final: 0.8552 (p) REVERT: A 173 TYR cc_start: 0.8779 (p90) cc_final: 0.8544 (p90) REVERT: A 202 THR cc_start: 0.9052 (m) cc_final: 0.8796 (t) REVERT: A 356 ASN cc_start: 0.8447 (p0) cc_final: 0.7954 (p0) REVERT: B 151 ARG cc_start: 0.7836 (tpt90) cc_final: 0.7279 (mtm-85) REVERT: B 543 ASN cc_start: 0.8036 (m-40) cc_final: 0.7581 (m110) REVERT: B 544 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7958 (mp) REVERT: B 577 GLN cc_start: 0.7293 (mt0) cc_final: 0.6865 (tm-30) REVERT: B 607 ASN cc_start: 0.6886 (m-40) cc_final: 0.6024 (p0) REVERT: C 49 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7894 (mm-30) REVERT: C 280 ASN cc_start: 0.7877 (m-40) cc_final: 0.7325 (t0) REVERT: C 584 GLU cc_start: 0.8228 (tt0) cc_final: 0.7963 (tt0) REVERT: C 632 ASP cc_start: 0.8884 (t70) cc_final: 0.8550 (t0) REVERT: H 28 PHE cc_start: 0.7981 (m-80) cc_final: 0.6784 (t80) REVERT: H 79 SER cc_start: 0.8649 (p) cc_final: 0.8277 (m) REVERT: H 82 SER cc_start: 0.9105 (m) cc_final: 0.8641 (p) REVERT: L 52 SER cc_start: 0.8564 (t) cc_final: 0.8090 (p) REVERT: L 93 SER cc_start: 0.8660 (p) cc_final: 0.8328 (m) outliers start: 41 outliers final: 28 residues processed: 254 average time/residue: 0.1207 time to fit residues: 47.4066 Evaluate side-chains 231 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 0.0370 chunk 154 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121321 restraints weight = 19201.452| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.70 r_work: 0.3157 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16027 Z= 0.135 Angle : 0.597 11.801 21885 Z= 0.290 Chirality : 0.046 0.310 2644 Planarity : 0.004 0.049 2653 Dihedral : 6.416 94.782 3490 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.14 % Allowed : 9.65 % Favored : 88.22 % 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 (0.20), residues: 1807 helix: 1.30 (0.28), residues: 370 sheet: -0.85 (0.21), residues: 568 loop : -1.10 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 298 TYR 0.019 0.001 TYR L 91 PHE 0.018 0.001 PHE H 78 TRP 0.014 0.001 TRP C 479 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (15921) covalent geometry : angle 0.56089 / 0.28 (21600) SS BOND : bond 0.00362 / 0.23 ( 33) SS BOND : angle 1.57286 / 1.06 ( 66) hydrogen bonds : bond 0.03407 / 2.31 ( 475) hydrogen bonds : angle 4.99047 / 3.54 ( 1302) link_ALPHA1-2 : bond 0.00248 / 0.13 ( 1) link_ALPHA1-2 : angle 2.48864 / 1.33 ( 3) link_ALPHA1-3 : bond 0.00911 / 0.48 ( 1) link_ALPHA1-3 : angle 0.82153 / 0.45 ( 3) link_ALPHA1-6 : bond 0.00938 / 0.49 ( 1) link_ALPHA1-6 : angle 1.51868 / 0.84 ( 3) link_BETA1-4 : bond 0.00443 / 0.25 ( 23) link_BETA1-4 : angle 1.50503 / 1.11 ( 69) link_NAG-ASN : bond 0.00280 / 0.15 ( 47) link_NAG-ASN : angle 2.14942 / 1.59 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 213 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7100 (pt0) REVERT: A 83 GLU cc_start: 0.8028 (pt0) cc_final: 0.7762 (pt0) REVERT: A 136 ASN cc_start: 0.7849 (t0) cc_final: 0.7515 (t0) REVERT: A 158 SER cc_start: 0.8787 (m) cc_final: 0.8521 (p) REVERT: A 202 THR cc_start: 0.8989 (m) cc_final: 0.8720 (t) REVERT: A 356 ASN cc_start: 0.8454 (p0) cc_final: 0.7971 (p0) REVERT: B 46 LYS cc_start: 0.8814 (mtmt) cc_final: 0.8486 (ptpt) REVERT: B 151 ARG cc_start: 0.7784 (tpt90) cc_final: 0.7265 (mtm-85) REVERT: B 419 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7705 (mtp180) REVERT: B 543 ASN cc_start: 0.7971 (m-40) cc_final: 0.7509 (m110) REVERT: B 544 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 577 GLN cc_start: 0.7251 (mt0) cc_final: 0.6820 (tm-30) REVERT: B 607 ASN cc_start: 0.6941 (m-40) cc_final: 0.6093 (p0) REVERT: C 49 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7918 (mm-30) REVERT: C 280 ASN cc_start: 0.7821 (m-40) cc_final: 0.7288 (t0) REVERT: C 318 TYR cc_start: 0.8856 (m-80) cc_final: 0.8539 (m-80) REVERT: C 584 GLU cc_start: 0.8196 (tt0) cc_final: 0.7902 (tt0) REVERT: C 632 ASP cc_start: 0.8840 (t70) cc_final: 0.8499 (t0) REVERT: H 28 PHE cc_start: 0.7953 (m-80) cc_final: 0.6786 (t80) REVERT: H 79 SER cc_start: 0.8618 (p) cc_final: 0.8269 (m) REVERT: H 82 SER cc_start: 0.9092 (m) cc_final: 0.8623 (p) REVERT: L 93 SER cc_start: 0.8671 (p) cc_final: 0.8314 (m) outliers start: 35 outliers final: 25 residues processed: 240 average time/residue: 0.1171 time to fit residues: 43.5611 Evaluate side-chains 224 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 115 optimal weight: 3.9990 chunk 180 optimal weight: 0.5980 chunk 109 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 ASN B 425 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.145611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118274 restraints weight = 19296.680| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.76 r_work: 0.3110 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16027 Z= 0.202 Angle : 0.648 12.020 21885 Z= 0.313 Chirality : 0.047 0.322 2644 Planarity : 0.004 0.050 2653 Dihedral : 6.551 96.306 3490 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.81 % Allowed : 9.77 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.20), residues: 1807 helix: 1.30 (0.28), residues: 370 sheet: -0.86 (0.21), residues: 544 loop : -1.16 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 298 TYR 0.021 0.002 TYR L 91 PHE 0.020 0.002 PHE H 78 TRP 0.015 0.001 TRP C 479 HIS 0.005 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (15921) covalent geometry : angle 0.61212 / 0.30 (21600) SS BOND : bond 0.00469 / 0.28 ( 33) SS BOND : angle 1.66047 / 1.11 ( 66) hydrogen bonds : bond 0.03679 / 2.49 ( 475) hydrogen bonds : angle 5.08594 / 3.60 ( 1302) link_ALPHA1-2 : bond 0.00445 / 0.23 ( 1) link_ALPHA1-2 : angle 2.68083 / 1.44 ( 3) link_ALPHA1-3 : bond 0.01102 / 0.58 ( 1) link_ALPHA1-3 : angle 0.94484 / 0.53 ( 3) link_ALPHA1-6 : bond 0.01028 / 0.54 ( 1) link_ALPHA1-6 : angle 1.56143 / 0.85 ( 3) link_BETA1-4 : bond 0.00457 / 0.27 ( 23) link_BETA1-4 : angle 1.59265 / 1.17 ( 69) link_NAG-ASN : bond 0.00340 / 0.19 ( 47) link_NAG-ASN : angle 2.25005 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7140 (pt0) REVERT: A 83 GLU cc_start: 0.8085 (pt0) cc_final: 0.7788 (pt0) REVERT: A 136 ASN cc_start: 0.7868 (t0) cc_final: 0.7506 (t0) REVERT: A 151 ARG cc_start: 0.8286 (tpp-160) cc_final: 0.8072 (mmt90) REVERT: A 158 SER cc_start: 0.8794 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 173 TYR cc_start: 0.8745 (p90) cc_final: 0.8505 (p90) REVERT: A 202 THR cc_start: 0.9104 (m) cc_final: 0.8872 (t) REVERT: A 356 ASN cc_start: 0.8475 (p0) cc_final: 0.7974 (p0) REVERT: B 46 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8330 (mtmm) REVERT: B 151 ARG cc_start: 0.7800 (tpt90) cc_final: 0.7271 (mtm-85) REVERT: B 425 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: B 430 ILE cc_start: 0.8417 (mt) cc_final: 0.8027 (tp) REVERT: B 543 ASN cc_start: 0.8026 (m-40) cc_final: 0.7581 (m110) REVERT: B 544 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (mp) REVERT: B 607 ASN cc_start: 0.6893 (m-40) cc_final: 0.6016 (p0) REVERT: C 280 ASN cc_start: 0.7811 (m-40) cc_final: 0.7282 (t0) REVERT: C 424 ILE cc_start: 0.8481 (pt) cc_final: 0.8229 (pt) REVERT: C 584 GLU cc_start: 0.8210 (tt0) cc_final: 0.7914 (tt0) REVERT: C 632 ASP cc_start: 0.8843 (t70) cc_final: 0.8497 (t0) REVERT: H 28 PHE cc_start: 0.8048 (m-80) cc_final: 0.6813 (t80) REVERT: H 79 SER cc_start: 0.8623 (p) cc_final: 0.8223 (m) REVERT: H 82 SER cc_start: 0.9131 (m) cc_final: 0.8667 (p) REVERT: L 93 SER cc_start: 0.8673 (p) cc_final: 0.8309 (m) outliers start: 46 outliers final: 37 residues processed: 232 average time/residue: 0.1250 time to fit residues: 44.7485 Evaluate side-chains 229 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 330 HIS Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 27 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 56 optimal weight: 0.0170 chunk 41 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 377 ASN B 425 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119482 restraints weight = 19174.090| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.71 r_work: 0.3139 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16027 Z= 0.143 Angle : 0.616 13.517 21885 Z= 0.297 Chirality : 0.046 0.308 2644 Planarity : 0.004 0.045 2653 Dihedral : 6.443 95.050 3490 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.63 % Allowed : 10.13 % Favored : 87.24 % 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 (0.20), residues: 1807 helix: 1.42 (0.28), residues: 370 sheet: -0.87 (0.21), residues: 560 loop : -1.17 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 81 TYR 0.019 0.001 TYR L 91 PHE 0.018 0.002 PHE A 468 TRP 0.016 0.001 TRP A 631 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (15921) covalent geometry : angle 0.57953 / 0.29 (21600) SS BOND : bond 0.00413 / 0.25 ( 33) SS BOND : angle 1.69322 / 1.13 ( 66) hydrogen bonds : bond 0.03420 / 2.32 ( 475) hydrogen bonds : angle 4.98562 / 3.53 ( 1302) link_ALPHA1-2 : bond 0.00228 / 0.12 ( 1) link_ALPHA1-2 : angle 2.53784 / 1.36 ( 3) link_ALPHA1-3 : bond 0.01082 / 0.57 ( 1) link_ALPHA1-3 : angle 0.86289 / 0.48 ( 3) link_ALPHA1-6 : bond 0.00918 / 0.48 ( 1) link_ALPHA1-6 : angle 1.47039 / 0.81 ( 3) link_BETA1-4 : bond 0.00458 / 0.26 ( 23) link_BETA1-4 : angle 1.50373 / 1.11 ( 69) link_NAG-ASN : bond 0.00309 / 0.16 ( 47) link_NAG-ASN : angle 2.18478 / 1.62 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7104 (pt0) REVERT: A 83 GLU cc_start: 0.8063 (pt0) cc_final: 0.7756 (pt0) REVERT: A 136 ASN cc_start: 0.7837 (t0) cc_final: 0.7484 (t0) REVERT: A 151 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.8029 (mmt90) REVERT: A 158 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8528 (p) REVERT: A 202 THR cc_start: 0.9102 (m) cc_final: 0.8855 (t) REVERT: A 356 ASN cc_start: 0.8461 (p0) cc_final: 0.7970 (p0) REVERT: A 490 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7444 (ptmt) REVERT: B 151 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7227 (mtm-85) REVERT: B 430 ILE cc_start: 0.8399 (mt) cc_final: 0.8113 (mm) REVERT: B 543 ASN cc_start: 0.8050 (m-40) cc_final: 0.7658 (m110) REVERT: B 544 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7862 (mp) REVERT: B 607 ASN cc_start: 0.6968 (m-40) cc_final: 0.6096 (p0) REVERT: C 95 MET cc_start: 0.8904 (ptm) cc_final: 0.8530 (ptm) REVERT: C 280 ASN cc_start: 0.7794 (m-40) cc_final: 0.7283 (t0) REVERT: C 424 ILE cc_start: 0.8457 (pt) cc_final: 0.8192 (pt) REVERT: C 584 GLU cc_start: 0.8177 (tt0) cc_final: 0.7884 (tt0) REVERT: C 632 ASP cc_start: 0.8820 (t70) cc_final: 0.8466 (t0) REVERT: H 28 PHE cc_start: 0.7995 (m-80) cc_final: 0.6795 (t80) REVERT: H 79 SER cc_start: 0.8588 (p) cc_final: 0.8198 (m) REVERT: H 82 SER cc_start: 0.9111 (m) cc_final: 0.8644 (p) REVERT: L 93 SER cc_start: 0.8658 (p) cc_final: 0.8287 (m) outliers start: 43 outliers final: 35 residues processed: 237 average time/residue: 0.1214 time to fit residues: 44.5629 Evaluate side-chains 232 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 194 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 156 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117160 restraints weight = 19215.715| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.86 r_work: 0.3106 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16027 Z= 0.179 Angle : 0.640 13.670 21885 Z= 0.309 Chirality : 0.047 0.314 2644 Planarity : 0.004 0.048 2653 Dihedral : 6.503 95.679 3490 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.93 % Allowed : 10.44 % Favored : 86.63 % 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: -0.89 (0.20), residues: 1807 helix: 1.36 (0.28), residues: 368 sheet: -0.90 (0.22), residues: 558 loop : -1.19 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 298 TYR 0.020 0.001 TYR L 91 PHE 0.021 0.002 PHE H 78 TRP 0.021 0.001 TRP A 631 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.18 (15921) covalent geometry : angle 0.60304 / 0.30 (21600) SS BOND : bond 0.00451 / 0.29 ( 33) SS BOND : angle 1.71509 / 1.14 ( 66) hydrogen bonds : bond 0.03580 / 2.43 ( 475) hydrogen bonds : angle 5.02890 / 3.55 ( 1302) link_ALPHA1-2 : bond 0.00286 / 0.15 ( 1) link_ALPHA1-2 : angle 2.59944 / 1.39 ( 3) link_ALPHA1-3 : bond 0.01074 / 0.57 ( 1) link_ALPHA1-3 : angle 0.88004 / 0.50 ( 3) link_ALPHA1-6 : bond 0.00995 / 0.52 ( 1) link_ALPHA1-6 : angle 1.50825 / 0.83 ( 3) link_BETA1-4 : bond 0.00458 / 0.27 ( 23) link_BETA1-4 : angle 1.54244 / 1.14 ( 69) link_NAG-ASN : bond 0.00324 / 0.18 ( 47) link_NAG-ASN : angle 2.24549 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 204 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7147 (pt0) REVERT: A 129 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8329 (mt) REVERT: A 136 ASN cc_start: 0.7833 (t0) cc_final: 0.7479 (t0) REVERT: A 158 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8561 (p) REVERT: A 173 TYR cc_start: 0.8725 (p90) cc_final: 0.8472 (p90) REVERT: A 202 THR cc_start: 0.9165 (m) cc_final: 0.8931 (t) REVERT: A 356 ASN cc_start: 0.8492 (p0) cc_final: 0.7992 (p0) REVERT: B 151 ARG cc_start: 0.7901 (tpt90) cc_final: 0.7388 (mtm-85) REVERT: B 430 ILE cc_start: 0.8451 (mt) cc_final: 0.8068 (tp) REVERT: B 543 ASN cc_start: 0.8030 (m-40) cc_final: 0.7654 (m110) REVERT: B 544 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 607 ASN cc_start: 0.7038 (m-40) cc_final: 0.6233 (p0) REVERT: C 95 MET cc_start: 0.8943 (ptm) cc_final: 0.8532 (ptm) REVERT: C 280 ASN cc_start: 0.7846 (m-40) cc_final: 0.7301 (t0) REVERT: C 424 ILE cc_start: 0.8477 (pt) cc_final: 0.8238 (pt) REVERT: C 584 GLU cc_start: 0.8187 (tt0) cc_final: 0.7894 (tt0) REVERT: C 632 ASP cc_start: 0.8844 (t70) cc_final: 0.8464 (t0) REVERT: H 28 PHE cc_start: 0.8055 (m-80) cc_final: 0.6748 (t80) REVERT: H 79 SER cc_start: 0.8626 (p) cc_final: 0.8227 (m) REVERT: H 82 SER cc_start: 0.9109 (m) cc_final: 0.8655 (p) REVERT: L 93 SER cc_start: 0.8710 (p) cc_final: 0.8333 (m) outliers start: 48 outliers final: 40 residues processed: 241 average time/residue: 0.1184 time to fit residues: 44.8036 Evaluate side-chains 228 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 4 optimal weight: 0.0060 chunk 134 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118568 restraints weight = 19303.467| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.81 r_work: 0.3128 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16027 Z= 0.135 Angle : 0.607 14.239 21885 Z= 0.292 Chirality : 0.045 0.289 2644 Planarity : 0.004 0.048 2653 Dihedral : 6.342 93.515 3490 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.26 % Allowed : 11.66 % Favored : 86.08 % 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: -0.80 (0.20), residues: 1807 helix: 1.44 (0.28), residues: 368 sheet: -0.81 (0.22), residues: 555 loop : -1.15 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 81 TYR 0.018 0.001 TYR L 91 PHE 0.018 0.002 PHE A 468 TRP 0.021 0.001 TRP A 631 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (15921) covalent geometry : angle 0.57196 / 0.28 (21600) SS BOND : bond 0.00388 / 0.23 ( 33) SS BOND : angle 1.43741 / 0.95 ( 66) hydrogen bonds : bond 0.03293 / 2.25 ( 475) hydrogen bonds : angle 4.91405 / 3.47 ( 1302) link_ALPHA1-2 : bond 0.00135 / 0.07 ( 1) link_ALPHA1-2 : angle 2.44713 / 1.31 ( 3) link_ALPHA1-3 : bond 0.01135 / 0.60 ( 1) link_ALPHA1-3 : angle 0.85688 / 0.48 ( 3) link_ALPHA1-6 : bond 0.00827 / 0.44 ( 1) link_ALPHA1-6 : angle 1.43122 / 0.79 ( 3) link_BETA1-4 : bond 0.00472 / 0.27 ( 23) link_BETA1-4 : angle 1.45400 / 1.07 ( 69) link_NAG-ASN : bond 0.00291 / 0.15 ( 47) link_NAG-ASN : angle 2.20090 / 1.64 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7130 (pt0) REVERT: A 129 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 136 ASN cc_start: 0.7766 (t0) cc_final: 0.7430 (t0) REVERT: A 158 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (p) REVERT: A 202 THR cc_start: 0.9155 (m) cc_final: 0.8896 (t) REVERT: A 356 ASN cc_start: 0.8492 (p0) cc_final: 0.7993 (p0) REVERT: B 151 ARG cc_start: 0.7855 (tpt90) cc_final: 0.7264 (mtm-85) REVERT: B 430 ILE cc_start: 0.8462 (mt) cc_final: 0.8080 (tp) REVERT: B 543 ASN cc_start: 0.7965 (m-40) cc_final: 0.7664 (m110) REVERT: B 544 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7799 (mp) REVERT: B 607 ASN cc_start: 0.7113 (m-40) cc_final: 0.6267 (p0) REVERT: C 95 MET cc_start: 0.8928 (ptm) cc_final: 0.8501 (ptm) REVERT: C 280 ASN cc_start: 0.7857 (m-40) cc_final: 0.7350 (t0) REVERT: C 424 ILE cc_start: 0.8432 (pt) cc_final: 0.8204 (pt) REVERT: C 584 GLU cc_start: 0.8167 (tt0) cc_final: 0.7873 (tt0) REVERT: C 632 ASP cc_start: 0.8801 (t70) cc_final: 0.8530 (t0) REVERT: H 28 PHE cc_start: 0.8033 (m-80) cc_final: 0.6742 (t80) REVERT: H 43 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7847 (mtpt) REVERT: H 79 SER cc_start: 0.8593 (p) cc_final: 0.8206 (m) REVERT: H 82 SER cc_start: 0.9113 (m) cc_final: 0.8651 (p) REVERT: L 93 SER cc_start: 0.8703 (p) cc_final: 0.8282 (m) outliers start: 37 outliers final: 30 residues processed: 230 average time/residue: 0.1205 time to fit residues: 43.3233 Evaluate side-chains 225 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 14 optimal weight: 0.0980 chunk 156 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 163 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN C 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120113 restraints weight = 19230.906| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.74 r_work: 0.3149 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 16027 Z= 0.129 Angle : 0.594 14.608 21885 Z= 0.286 Chirality : 0.045 0.285 2644 Planarity : 0.004 0.045 2653 Dihedral : 6.209 91.610 3490 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.56 % Allowed : 11.17 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.20), residues: 1807 helix: 1.52 (0.28), residues: 368 sheet: -0.75 (0.22), residues: 555 loop : -1.12 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 81 TYR 0.018 0.001 TYR L 91 PHE 0.018 0.001 PHE H 78 TRP 0.020 0.001 TRP A 631 HIS 0.004 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (15921) covalent geometry : angle 0.56101 / 0.28 (21600) SS BOND : bond 0.00376 / 0.22 ( 33) SS BOND : angle 1.33704 / 0.88 ( 66) hydrogen bonds : bond 0.03225 / 2.20 ( 475) hydrogen bonds : angle 4.85896 / 3.44 ( 1302) link_ALPHA1-2 : bond 0.00170 / 0.09 ( 1) link_ALPHA1-2 : angle 2.38886 / 1.28 ( 3) link_ALPHA1-3 : bond 0.00987 / 0.52 ( 1) link_ALPHA1-3 : angle 0.77247 / 0.43 ( 3) link_ALPHA1-6 : bond 0.00855 / 0.45 ( 1) link_ALPHA1-6 : angle 1.36822 / 0.76 ( 3) link_BETA1-4 : bond 0.00458 / 0.26 ( 23) link_BETA1-4 : angle 1.43376 / 1.06 ( 69) link_NAG-ASN : bond 0.00288 / 0.15 ( 47) link_NAG-ASN : angle 2.14089 / 1.59 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7101 (pt0) REVERT: A 129 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8283 (mt) REVERT: A 136 ASN cc_start: 0.7863 (t0) cc_final: 0.7537 (t0) REVERT: A 158 SER cc_start: 0.8782 (m) cc_final: 0.8546 (p) REVERT: A 202 THR cc_start: 0.9138 (m) cc_final: 0.8907 (t) REVERT: A 356 ASN cc_start: 0.8461 (p0) cc_final: 0.7960 (p0) REVERT: A 490 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7403 (ptmt) REVERT: B 151 ARG cc_start: 0.7856 (tpt90) cc_final: 0.7250 (mtm-85) REVERT: B 430 ILE cc_start: 0.8463 (mt) cc_final: 0.8096 (tp) REVERT: B 543 ASN cc_start: 0.7982 (m-40) cc_final: 0.7773 (m110) REVERT: B 544 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7806 (mp) REVERT: B 607 ASN cc_start: 0.7107 (m-40) cc_final: 0.6297 (p0) REVERT: C 91 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6859 (mm-30) REVERT: C 95 MET cc_start: 0.8920 (ptm) cc_final: 0.8504 (ptm) REVERT: C 280 ASN cc_start: 0.7875 (m-40) cc_final: 0.7369 (t0) REVERT: C 424 ILE cc_start: 0.8429 (pt) cc_final: 0.8200 (pt) REVERT: C 632 ASP cc_start: 0.8786 (t70) cc_final: 0.8526 (t0) REVERT: H 28 PHE cc_start: 0.7979 (m-80) cc_final: 0.6751 (t80) REVERT: H 43 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7899 (mtpt) REVERT: H 79 SER cc_start: 0.8575 (p) cc_final: 0.8220 (m) REVERT: H 82 SER cc_start: 0.9148 (m) cc_final: 0.8679 (p) REVERT: L 93 SER cc_start: 0.8647 (p) cc_final: 0.8208 (m) outliers start: 42 outliers final: 39 residues processed: 224 average time/residue: 0.1192 time to fit residues: 41.8877 Evaluate side-chains 233 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 47 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN B 425 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.114736 restraints weight = 19419.619| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.78 r_work: 0.3076 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16027 Z= 0.230 Angle : 0.683 12.696 21885 Z= 0.332 Chirality : 0.048 0.325 2644 Planarity : 0.005 0.064 2653 Dihedral : 6.630 95.902 3490 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.75 % Allowed : 11.29 % Favored : 85.96 % 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: -0.96 (0.20), residues: 1807 helix: 1.30 (0.28), residues: 368 sheet: -0.91 (0.21), residues: 561 loop : -1.26 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 81 TYR 0.021 0.002 TYR L 91 PHE 0.020 0.002 PHE H 78 TRP 0.033 0.002 TRP A 631 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (15921) covalent geometry : angle 0.64727 / 0.32 (21600) SS BOND : bond 0.00467 / 0.28 ( 33) SS BOND : angle 1.58379 / 1.03 ( 66) hydrogen bonds : bond 0.03835 / 2.61 ( 475) hydrogen bonds : angle 5.13316 / 3.62 ( 1302) link_ALPHA1-2 : bond 0.00343 / 0.18 ( 1) link_ALPHA1-2 : angle 2.74355 / 1.47 ( 3) link_ALPHA1-3 : bond 0.01040 / 0.55 ( 1) link_ALPHA1-3 : angle 0.97171 / 0.55 ( 3) link_ALPHA1-6 : bond 0.01063 / 0.56 ( 1) link_ALPHA1-6 : angle 1.51498 / 0.83 ( 3) link_BETA1-4 : bond 0.00450 / 0.27 ( 23) link_BETA1-4 : angle 1.61783 / 1.19 ( 69) link_NAG-ASN : bond 0.00381 / 0.23 ( 47) link_NAG-ASN : angle 2.33593 / 1.74 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7183 (pt0) REVERT: A 129 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 136 ASN cc_start: 0.7670 (t0) cc_final: 0.7337 (t0) REVERT: A 158 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 173 TYR cc_start: 0.8723 (p90) cc_final: 0.8488 (p90) REVERT: A 202 THR cc_start: 0.9209 (m) cc_final: 0.8984 (t) REVERT: A 356 ASN cc_start: 0.8481 (p0) cc_final: 0.7983 (p0) REVERT: A 490 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7340 (ptmt) REVERT: A 653 GLN cc_start: 0.6678 (tt0) cc_final: 0.6244 (mt0) REVERT: B 151 ARG cc_start: 0.7892 (tpt90) cc_final: 0.7222 (mtm-85) REVERT: B 430 ILE cc_start: 0.8453 (mt) cc_final: 0.8105 (tp) REVERT: B 543 ASN cc_start: 0.7999 (m-40) cc_final: 0.7674 (m110) REVERT: B 544 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7781 (mp) REVERT: B 607 ASN cc_start: 0.7004 (m-40) cc_final: 0.6161 (p0) REVERT: C 91 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6889 (mm-30) REVERT: C 280 ASN cc_start: 0.7894 (m-40) cc_final: 0.7382 (t0) REVERT: C 424 ILE cc_start: 0.8510 (pt) cc_final: 0.8285 (pt) REVERT: C 584 GLU cc_start: 0.8162 (tt0) cc_final: 0.7909 (tt0) REVERT: C 632 ASP cc_start: 0.8759 (t70) cc_final: 0.8374 (t0) REVERT: H 28 PHE cc_start: 0.8076 (m-80) cc_final: 0.6662 (t80) REVERT: H 43 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7860 (mtpt) REVERT: H 79 SER cc_start: 0.8665 (p) cc_final: 0.8212 (m) REVERT: H 82 SER cc_start: 0.9079 (m) cc_final: 0.8606 (p) REVERT: L 93 SER cc_start: 0.8761 (p) cc_final: 0.8393 (m) outliers start: 45 outliers final: 38 residues processed: 231 average time/residue: 0.1236 time to fit residues: 43.7053 Evaluate side-chains 236 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 490 LYS Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 331 CYS Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 388 SER Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 65 optimal weight: 0.0030 chunk 134 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120003 restraints weight = 19160.517| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.73 r_work: 0.3146 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 16027 Z= 0.122 Angle : 0.603 14.915 21885 Z= 0.292 Chirality : 0.045 0.278 2644 Planarity : 0.004 0.053 2653 Dihedral : 6.353 93.171 3490 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.20 % Allowed : 11.97 % Favored : 85.84 % 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: -0.80 (0.20), residues: 1807 helix: 1.50 (0.28), residues: 368 sheet: -0.81 (0.21), residues: 570 loop : -1.18 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 81 TYR 0.017 0.001 TYR L 91 PHE 0.017 0.001 PHE H 78 TRP 0.027 0.001 TRP A 631 HIS 0.003 0.001 HIS L 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.12 (15921) covalent geometry : angle 0.57087 / 0.28 (21600) SS BOND : bond 0.00378 / 0.23 ( 33) SS BOND : angle 1.37522 / 0.90 ( 66) hydrogen bonds : bond 0.03243 / 2.22 ( 475) hydrogen bonds : angle 4.88286 / 3.45 ( 1302) link_ALPHA1-2 : bond 0.00085 / 0.04 ( 1) link_ALPHA1-2 : angle 2.41333 / 1.29 ( 3) link_ALPHA1-3 : bond 0.01004 / 0.53 ( 1) link_ALPHA1-3 : angle 0.73828 / 0.41 ( 3) link_ALPHA1-6 : bond 0.00758 / 0.40 ( 1) link_ALPHA1-6 : angle 1.39143 / 0.78 ( 3) link_BETA1-4 : bond 0.00477 / 0.27 ( 23) link_BETA1-4 : angle 1.43267 / 1.06 ( 69) link_NAG-ASN : bond 0.00285 / 0.15 ( 47) link_NAG-ASN : angle 2.12590 / 1.57 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.68 seconds wall clock time: 76 minutes 5.59 seconds (4565.59 seconds total)