Starting phenix.real_space_refine on Thu Sep 18 21:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879.map" model { file = "/net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9aug_43879/09_2025/9aug_43879_neut.cif" } resolution = 3.8 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= 0.001 sd= 0.029 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 135 5.16 5 C 12591 2.51 5 N 3342 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20211 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "B" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "C" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3590 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 23, 'TRANS': 436} Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "F" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 996 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "L" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 796 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "M" 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: "N" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "O" 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: "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: 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: "S" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "T" 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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Y" 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 4.44, per 1000 atoms: 0.22 Number of scatterers: 20211 At special positions: 0 Unit cell: (146.88, 160.92, 157.68, 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 135 16.00 O 4143 8.00 N 3342 7.00 C 12591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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=2.03 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=2.05 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 385 " - pdb=" SG CYS A 418 " distance=2.05 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 74 " distance=2.04 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.05 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS E 605 " 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=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.05 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 385 " - pdb=" SG CYS C 418 " distance=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 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 N 4 " - " MAN N 5 " " MAN S 4 " - " MAN S 5 " " MAN X 4 " - " MAN X 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 6 " - " MAN X 7 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA R 3 " - " MAN R 5 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " " BMA W 3 " - " MAN W 5 " " BMA X 3 " - " MAN X 6 " " MAN X 6 " - " MAN X 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 386 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 362 " " NAG A 605 " - " ASN A 276 " " NAG A 606 " - " ASN A 88 " " NAG A 607 " - " ASN A 241 " " NAG A 608 " - " ASN A 448 " " NAG A 609 " - " ASN A 442 " " NAG B 601 " - " ASN B 386 " " NAG B 602 " - " ASN B 392 " " NAG B 603 " - " ASN B 160 " " NAG B 604 " - " ASN B 362 " " NAG B 605 " - " ASN B 276 " " NAG B 606 " - " ASN B 88 " " NAG B 607 " - " ASN B 241 " " NAG B 608 " - " ASN B 448 " " NAG B 609 " - " ASN B 442 " " NAG C 601 " - " ASN C 386 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 362 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 241 " " NAG C 608 " - " ASN C 448 " " NAG C 609 " - " ASN C 442 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 332 " " NAG O 1 " - " ASN A 300 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 197 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 332 " " NAG T 1 " - " ASN B 300 " " NAG U 1 " - " ASN B 156 " " NAG V 1 " - " ASN B 197 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 332 " " NAG Y 1 " - " ASN C 300 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN C 197 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 627.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4518 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 46 sheets defined 18.4% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.039A pdb=" N GLU A 62 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.852A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.710A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.640A 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 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.735A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.511A pdb=" N ASN A 408 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 409' Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.099A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLY A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 483 removed outlier: 4.147A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 removed outlier: 3.632A pdb=" N TYR B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 Processing helix chain 'B' and resid 335 through 350 Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.587A pdb=" N THR B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 406 through 411 removed outlier: 3.909A pdb=" N SER B 409 " --> pdb=" O SER B 406 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 411' Processing helix chain 'B' and resid 475 through 482 removed outlier: 4.351A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.580A pdb=" N ALA C 60 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 62 " --> pdb=" O ARG C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 57 through 62' Processing helix chain 'C' and resid 98 through 115 removed outlier: 4.249A pdb=" N ASP C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.610A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.118A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.205A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 3.902A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 542 removed outlier: 3.515A pdb=" N ARG D 542 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 570 through 596 removed outlier: 4.122A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.638A pdb=" N ILE D 622 " --> pdb=" O ASN D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.545A pdb=" N TRP D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.544A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.879A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 536 " --> pdb=" O ALA E 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 536' Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.175A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 595 Processing helix chain 'E' and resid 618 through 626 Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.713A pdb=" N TRP E 631 " --> pdb=" O THR E 627 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 636 " --> pdb=" O ASP E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 664 removed outlier: 3.623A pdb=" N ILE E 642 " --> pdb=" O TYR E 638 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 removed outlier: 3.921A pdb=" N ALA F 541 " --> pdb=" O LEU F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 4.615A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.650A pdb=" N ILE F 622 " --> pdb=" O ASN F 618 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.893A pdb=" N TRP F 631 " --> pdb=" O THR F 627 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 664 removed outlier: 3.964A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.070A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.561A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.133A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.594A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.518A pdb=" N LEU A 84 " --> pdb=" O THR A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.736A pdb=" N SER A 56 " --> pdb=" O VAL A 75 " (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 129 through 130 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 159 through 162 Processing sheet with id=AA8, first strand: chain 'A' and resid 202 through 203 removed outlier: 7.540A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.614A pdb=" N THR A 357 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N PHE A 468 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.366A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 421 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 384 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 294 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 304 through 308 Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.625A pdb=" N LEU B 84 " --> pdb=" O THR B 244 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 44 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 494 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N VAL B 42 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N VAL B 496 " --> pdb=" O TYR B 40 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N TYR B 40 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N VAL B 38 " --> pdb=" O PRO B 498 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL B 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR E 606 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 159 through 162 Processing sheet with id=AB7, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB8, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.312A pdb=" N THR B 357 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N PHE B 468 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 360 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 393 " --> pdb=" O TYR B 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 294 through 296 removed outlier: 3.886A pdb=" N ALA B 329 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG B 419 " --> pdb=" O TYR B 384 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 384 " --> pdb=" O ARG B 419 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 removed outlier: 9.187A pdb=" N VAL C 489 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TRP C 45 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ILE C 491 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.600A pdb=" N SER C 56 " --> pdb=" O VAL C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AC6, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC7, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AC8, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.405A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.936A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.936A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 357 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE C 468 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 393 " --> pdb=" O TYR C 361 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 413 through 418 removed outlier: 4.003A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 294 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 304 through 308 Processing sheet with id=AD4, first strand: chain 'C' and resid 374 through 378 Processing sheet with id=AD5, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.275A pdb=" N TYR G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N MET G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TRP G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU G 46 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TRP G 50 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN G 59 " --> pdb=" O TRP G 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.753A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP H 50 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN H 59 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11 removed outlier: 5.339A pdb=" N TYR I 33 " --> pdb=" O GLY I 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TRP I 50 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN I 59 " --> pdb=" O TRP I 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 9 through 12 removed outlier: 7.098A pdb=" N TRP J 37 " --> pdb=" O MET J 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AE4, first strand: chain 'J' and resid 17 through 23 Processing sheet with id=AE5, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AE6, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.681A pdb=" N MET K 49 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 47 through 50 removed outlier: 3.681A pdb=" N MET K 49 " --> pdb=" O TRP K 37 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TRP K 37 " --> pdb=" O MET K 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA K 86 " --> pdb=" O LEU K 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU K 107 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR K 88 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR K 105 " --> pdb=" O TYR K 88 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.699A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L 39 " --> pdb=" O LYS L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AF1, first strand: chain 'L' and resid 17 through 23 623 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.27 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6362 1.35 - 1.48: 5486 1.48 - 1.61: 8590 1.61 - 1.74: 1 1.74 - 1.87: 183 Bond restraints: 20622 Sorted by residual: bond pdb=" C LYS A 117 " pdb=" N PRO A 118 " ideal model delta sigma weight residual 1.331 1.378 -0.046 7.90e-03 1.60e+04 3.40e+01 bond pdb=" C1 NAG C 606 " pdb=" O5 NAG C 606 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C1 MAN X 4 " pdb=" C2 MAN X 4 " ideal model delta sigma weight residual 1.526 1.579 -0.053 2.00e-02 2.50e+03 6.90e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.30e+00 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 27000 2.41 - 4.82: 824 4.82 - 7.23: 153 7.23 - 9.64: 34 9.64 - 12.05: 9 Bond angle restraints: 28020 Sorted by residual: angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 125.88 -11.48 2.30e+00 1.89e-01 2.49e+01 angle pdb=" CA ARG A 166 " pdb=" CB ARG A 166 " pdb=" CG ARG A 166 " ideal model delta sigma weight residual 114.10 123.71 -9.61 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA CYS C 247 " pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 114.40 125.38 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C SER E 615 " pdb=" N ASN E 616 " pdb=" CA ASN E 616 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C ASN C 67 " pdb=" N VAL C 68 " pdb=" CA VAL C 68 " ideal model delta sigma weight residual 121.97 129.81 -7.84 1.80e+00 3.09e-01 1.90e+01 ... (remaining 28015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.33: 12296 23.33 - 46.67: 865 46.67 - 70.00: 118 70.00 - 93.34: 83 93.34 - 116.67: 75 Dihedral angle restraints: 13437 sinusoidal: 6369 harmonic: 7068 Sorted by residual: dihedral pdb=" CB CYS B 54 " pdb=" SG CYS B 54 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual -86.00 -22.34 -63.66 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 49.25 43.75 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CB CYS B 385 " pdb=" SG CYS B 385 " pdb=" SG CYS B 418 " pdb=" CB CYS B 418 " ideal model delta sinusoidal sigma weight residual 93.00 49.46 43.54 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 13434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2771 0.073 - 0.147: 515 0.147 - 0.220: 73 0.220 - 0.294: 19 0.294 - 0.367: 6 Chirality restraints: 3384 Sorted by residual: chirality pdb=" C1 NAG C 606 " pdb=" ND2 ASN C 88 " pdb=" C2 NAG C 606 " pdb=" O5 NAG C 606 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C1 MAN X 4 " pdb=" O3 BMA X 3 " pdb=" C2 MAN X 4 " pdb=" O5 MAN X 4 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 3.29e+00 chirality pdb=" CB VAL C 430 " pdb=" CA VAL C 430 " pdb=" CG1 VAL C 430 " pdb=" CG2 VAL C 430 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 3381 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 69 " 0.017 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP B 69 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP B 69 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 69 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 69 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 69 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 69 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 69 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 69 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 69 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.022 2.00e-02 2.50e+03 2.16e-02 1.17e+01 pdb=" CG TRP H 36 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 117 " -0.012 2.00e-02 2.50e+03 1.99e-02 9.88e+00 pdb=" CG TRP I 117 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP I 117 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP I 117 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 117 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP I 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP I 117 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 117 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 117 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP I 117 " 0.009 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4708 2.80 - 3.32: 16641 3.32 - 3.85: 31876 3.85 - 4.37: 33310 4.37 - 4.90: 60753 Nonbonded interactions: 147288 Sorted by model distance: nonbonded pdb=" OG1 THR E 627 " pdb=" OE1 GLN E 630 " model vdw 2.270 3.040 nonbonded pdb=" OG SER C 185 " pdb=" O THR C 185b" model vdw 2.285 3.040 nonbonded pdb=" OG SER B 256 " pdb=" O LEU B 259 " model vdw 2.291 3.040 nonbonded pdb=" OG1 THR L 5 " pdb=" OG1 THR L 23 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR F 627 " pdb=" OE1 GLN F 630 " model vdw 2.295 3.040 ... (remaining 147283 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'S' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.940 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.006 0.109 20745 Z= 0.280 Angle : 1.036 12.754 28353 Z= 0.504 Chirality : 0.061 0.367 3384 Planarity : 0.006 0.117 3456 Dihedral : 18.451 116.672 8811 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.15), residues: 2427 helix: -1.41 (0.22), residues: 375 sheet: -0.52 (0.21), residues: 615 loop : -2.55 (0.14), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 72 TYR 0.036 0.002 TYR C 486 PHE 0.029 0.002 PHE B 317 TRP 0.058 0.003 TRP B 69 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00583 (20622) covalent geometry : angle 0.99993 (28020) SS BOND : bond 0.00786 ( 36) SS BOND : angle 2.00405 ( 72) hydrogen bonds : bond 0.14583 ( 604) hydrogen bonds : angle 6.58668 ( 1674) link_ALPHA1-2 : bond 0.00541 ( 3) link_ALPHA1-2 : angle 2.95041 ( 9) link_ALPHA1-3 : bond 0.00537 ( 9) link_ALPHA1-3 : angle 1.60944 ( 27) link_ALPHA1-6 : bond 0.00364 ( 9) link_ALPHA1-6 : angle 1.52587 ( 27) link_BETA1-4 : bond 0.00720 ( 24) link_BETA1-4 : angle 1.98311 ( 72) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 3.61218 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 647 GLU cc_start: 0.7513 (tt0) cc_final: 0.7278 (tt0) REVERT: E 538 THR cc_start: 0.9223 (p) cc_final: 0.8954 (p) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1368 time to fit residues: 85.4336 Evaluate side-chains 330 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 330 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 656 ASN I 52 ASN J 40 GLN K 16 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.142605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.112662 restraints weight = 32670.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113310 restraints weight = 30064.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114224 restraints weight = 26778.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114665 restraints weight = 21939.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114874 restraints weight = 21045.813| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20745 Z= 0.185 Angle : 0.704 9.723 28353 Z= 0.338 Chirality : 0.047 0.385 3384 Planarity : 0.004 0.061 3456 Dihedral : 14.145 112.501 4413 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.70 % Allowed : 10.89 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.18 (0.16), residues: 2427 helix: -0.38 (0.26), residues: 399 sheet: -0.40 (0.21), residues: 633 loop : -2.40 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 72 TYR 0.022 0.001 TYR K 51 PHE 0.025 0.002 PHE B 317 TRP 0.024 0.002 TRP I 117 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00432 (20622) covalent geometry : angle 0.66397 (28020) SS BOND : bond 0.00835 ( 36) SS BOND : angle 1.10263 ( 72) hydrogen bonds : bond 0.03748 ( 604) hydrogen bonds : angle 5.19438 ( 1674) link_ALPHA1-2 : bond 0.00798 ( 3) link_ALPHA1-2 : angle 3.41738 ( 9) link_ALPHA1-3 : bond 0.01063 ( 9) link_ALPHA1-3 : angle 2.14386 ( 27) link_ALPHA1-6 : bond 0.00640 ( 9) link_ALPHA1-6 : angle 1.64482 ( 27) link_BETA1-4 : bond 0.00463 ( 24) link_BETA1-4 : angle 2.04889 ( 72) link_NAG-ASN : bond 0.00412 ( 42) link_NAG-ASN : angle 2.83994 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 347 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8331 (tp) cc_final: 0.7981 (tt) REVERT: A 425 ASN cc_start: 0.7684 (t0) cc_final: 0.7463 (t0) REVERT: B 317 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8234 (p90) REVERT: C 504 ARG cc_start: 0.6234 (tmt170) cc_final: 0.5987 (tmt170) REVERT: D 540 GLN cc_start: 0.8259 (tt0) cc_final: 0.7984 (tm-30) REVERT: E 530 MET cc_start: 0.7011 (tpt) cc_final: 0.6501 (tpt) REVERT: E 538 THR cc_start: 0.9275 (p) cc_final: 0.9053 (p) REVERT: E 596 TRP cc_start: 0.7491 (p90) cc_final: 0.7114 (p90) REVERT: E 623 TRP cc_start: 0.7764 (m100) cc_final: 0.7379 (m100) REVERT: F 589 ASP cc_start: 0.8156 (t0) cc_final: 0.7850 (t0) REVERT: G 12 LYS cc_start: 0.7687 (mmmm) cc_final: 0.7332 (mmmm) REVERT: G 73 ASP cc_start: 0.7832 (t0) cc_final: 0.7589 (t0) outliers start: 36 outliers final: 27 residues processed: 368 average time/residue: 0.1331 time to fit residues: 77.1156 Evaluate side-chains 351 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 323 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 158 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 chunk 105 optimal weight: 1.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113777 restraints weight = 32951.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114450 restraints weight = 28616.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115456 restraints weight = 25436.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.115881 restraints weight = 21122.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.116055 restraints weight = 19516.885| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20745 Z= 0.121 Angle : 0.619 9.422 28353 Z= 0.299 Chirality : 0.045 0.359 3384 Planarity : 0.004 0.045 3456 Dihedral : 12.322 114.265 4413 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.60 % Allowed : 13.15 % Favored : 85.24 % 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 aren not related in a simple way. whole: -1.91 (0.17), residues: 2427 helix: 0.45 (0.29), residues: 378 sheet: -0.36 (0.21), residues: 648 loop : -2.34 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 72 TYR 0.015 0.001 TYR K 51 PHE 0.020 0.001 PHE B 317 TRP 0.024 0.001 TRP H 36 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00276 (20622) covalent geometry : angle 0.58225 (28020) SS BOND : bond 0.00376 ( 36) SS BOND : angle 0.94047 ( 72) hydrogen bonds : bond 0.03243 ( 604) hydrogen bonds : angle 4.86973 ( 1674) link_ALPHA1-2 : bond 0.00968 ( 3) link_ALPHA1-2 : angle 1.99849 ( 9) link_ALPHA1-3 : bond 0.01090 ( 9) link_ALPHA1-3 : angle 1.83122 ( 27) link_ALPHA1-6 : bond 0.00662 ( 9) link_ALPHA1-6 : angle 1.58516 ( 27) link_BETA1-4 : bond 0.00506 ( 24) link_BETA1-4 : angle 1.75540 ( 72) link_NAG-ASN : bond 0.00386 ( 42) link_NAG-ASN : angle 2.65416 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 352 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8359 (tp) cc_final: 0.8013 (tt) REVERT: D 540 GLN cc_start: 0.8223 (tt0) cc_final: 0.7776 (tm-30) REVERT: D 625 ASN cc_start: 0.7718 (t0) cc_final: 0.7444 (t0) REVERT: E 530 MET cc_start: 0.6928 (tpt) cc_final: 0.6646 (tpt) REVERT: E 538 THR cc_start: 0.9258 (p) cc_final: 0.9015 (p) REVERT: E 596 TRP cc_start: 0.7473 (p90) cc_final: 0.7020 (p90) REVERT: F 589 ASP cc_start: 0.8243 (t0) cc_final: 0.7964 (t0) REVERT: F 632 ASP cc_start: 0.8560 (t0) cc_final: 0.8330 (t0) REVERT: J 38 TYR cc_start: 0.8653 (m-80) cc_final: 0.8400 (m-80) REVERT: L 38 TYR cc_start: 0.7972 (m-80) cc_final: 0.7693 (m-80) outliers start: 34 outliers final: 28 residues processed: 372 average time/residue: 0.1419 time to fit residues: 82.9341 Evaluate side-chains 359 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 138 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 chunk 56 optimal weight: 0.0020 chunk 161 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 98 optimal weight: 4.9990 chunk 135 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 1.0088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.112795 restraints weight = 32703.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113792 restraints weight = 28620.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114251 restraints weight = 24886.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114887 restraints weight = 21460.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.115151 restraints weight = 19738.642| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20745 Z= 0.135 Angle : 0.626 9.354 28353 Z= 0.302 Chirality : 0.045 0.358 3384 Planarity : 0.004 0.049 3456 Dihedral : 11.580 113.892 4413 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.03 % Allowed : 14.99 % Favored : 82.98 % 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 aren not related in a simple way. whole: -1.79 (0.17), residues: 2427 helix: 0.60 (0.29), residues: 384 sheet: -0.28 (0.21), residues: 648 loop : -2.29 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 63 TYR 0.018 0.001 TYR K 51 PHE 0.010 0.001 PHE A 317 TRP 0.020 0.001 TRP F 571 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00314 (20622) covalent geometry : angle 0.58953 (28020) SS BOND : bond 0.00430 ( 36) SS BOND : angle 1.02578 ( 72) hydrogen bonds : bond 0.03181 ( 604) hydrogen bonds : angle 4.68439 ( 1674) link_ALPHA1-2 : bond 0.00904 ( 3) link_ALPHA1-2 : angle 2.14988 ( 9) link_ALPHA1-3 : bond 0.01012 ( 9) link_ALPHA1-3 : angle 1.93569 ( 27) link_ALPHA1-6 : bond 0.00671 ( 9) link_ALPHA1-6 : angle 1.60100 ( 27) link_BETA1-4 : bond 0.00505 ( 24) link_BETA1-4 : angle 1.61671 ( 72) link_NAG-ASN : bond 0.00381 ( 42) link_NAG-ASN : angle 2.64629 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 344 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8352 (tp) cc_final: 0.8007 (tt) REVERT: B 180 ASP cc_start: 0.8798 (m-30) cc_final: 0.8384 (t0) REVERT: C 342 LEU cc_start: 0.7125 (tt) cc_final: 0.6443 (tt) REVERT: D 540 GLN cc_start: 0.8206 (tt0) cc_final: 0.7820 (tm-30) REVERT: D 625 ASN cc_start: 0.7762 (t0) cc_final: 0.7427 (t0) REVERT: E 596 TRP cc_start: 0.7495 (p90) cc_final: 0.6965 (p90) REVERT: F 589 ASP cc_start: 0.8311 (t0) cc_final: 0.8047 (t0) REVERT: F 632 ASP cc_start: 0.8550 (t0) cc_final: 0.8285 (t0) REVERT: F 635 ILE cc_start: 0.8500 (tp) cc_final: 0.8299 (tt) REVERT: G 115 ASP cc_start: 0.8360 (t0) cc_final: 0.7805 (t0) REVERT: I 12 LYS cc_start: 0.8443 (mmmm) cc_final: 0.7919 (mmmm) REVERT: L 38 TYR cc_start: 0.7973 (m-80) cc_final: 0.7719 (m-80) outliers start: 43 outliers final: 38 residues processed: 369 average time/residue: 0.1376 time to fit residues: 78.9784 Evaluate side-chains 366 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 328 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 48 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 221 optimal weight: 0.2980 chunk 119 optimal weight: 3.9990 chunk 180 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112985 restraints weight = 32619.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113569 restraints weight = 29672.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114598 restraints weight = 26186.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115020 restraints weight = 21590.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.115259 restraints weight = 20692.028| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20745 Z= 0.125 Angle : 0.619 10.187 28353 Z= 0.297 Chirality : 0.045 0.350 3384 Planarity : 0.003 0.046 3456 Dihedral : 11.026 112.677 4413 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.92 % Allowed : 15.79 % Favored : 81.28 % 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 aren not related in a simple way. whole: -1.58 (0.17), residues: 2427 helix: 1.06 (0.29), residues: 369 sheet: -0.22 (0.21), residues: 648 loop : -2.16 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 63 TYR 0.022 0.001 TYR G 116 PHE 0.010 0.001 PHE A 317 TRP 0.026 0.001 TRP H 36 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00288 (20622) covalent geometry : angle 0.58522 (28020) SS BOND : bond 0.00373 ( 36) SS BOND : angle 0.92294 ( 72) hydrogen bonds : bond 0.03058 ( 604) hydrogen bonds : angle 4.57067 ( 1674) link_ALPHA1-2 : bond 0.00989 ( 3) link_ALPHA1-2 : angle 2.05655 ( 9) link_ALPHA1-3 : bond 0.01033 ( 9) link_ALPHA1-3 : angle 1.88269 ( 27) link_ALPHA1-6 : bond 0.00735 ( 9) link_ALPHA1-6 : angle 1.55767 ( 27) link_BETA1-4 : bond 0.00515 ( 24) link_BETA1-4 : angle 1.48833 ( 72) link_NAG-ASN : bond 0.00381 ( 42) link_NAG-ASN : angle 2.58972 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 349 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8344 (tp) cc_final: 0.8007 (tt) REVERT: B 180 ASP cc_start: 0.8782 (m-30) cc_final: 0.8338 (t0) REVERT: C 104 MET cc_start: 0.8597 (tpp) cc_final: 0.8377 (tpt) REVERT: C 154 MET cc_start: 0.8794 (mtt) cc_final: 0.8487 (mtt) REVERT: C 342 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6529 (tt) REVERT: C 475 MET cc_start: 0.8456 (tpp) cc_final: 0.8158 (tpp) REVERT: D 624 ASP cc_start: 0.7869 (m-30) cc_final: 0.7583 (p0) REVERT: E 596 TRP cc_start: 0.7440 (p90) cc_final: 0.6861 (p90) REVERT: F 530 MET cc_start: 0.7477 (mmt) cc_final: 0.7075 (tpt) REVERT: F 589 ASP cc_start: 0.8218 (t0) cc_final: 0.7907 (t0) REVERT: F 617 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7908 (ttp-170) REVERT: F 632 ASP cc_start: 0.8492 (t0) cc_final: 0.8203 (t0) REVERT: F 635 ILE cc_start: 0.8543 (tp) cc_final: 0.8333 (tt) REVERT: I 12 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8016 (mmmm) REVERT: L 38 TYR cc_start: 0.7921 (m-80) cc_final: 0.7703 (m-10) outliers start: 62 outliers final: 46 residues processed: 390 average time/residue: 0.1383 time to fit residues: 85.1197 Evaluate side-chains 379 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 617 ARG Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain F residue 649 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 78 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 215 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 HIS C 66 HIS C 72 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN L 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108845 restraints weight = 32880.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.109301 restraints weight = 28585.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109959 restraints weight = 26408.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110453 restraints weight = 22455.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110641 restraints weight = 21025.598| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20745 Z= 0.197 Angle : 0.692 9.330 28353 Z= 0.334 Chirality : 0.047 0.352 3384 Planarity : 0.004 0.075 3456 Dihedral : 11.004 115.116 4413 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.30 % Allowed : 16.69 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.17), residues: 2427 helix: 0.77 (0.29), residues: 387 sheet: -0.23 (0.21), residues: 654 loop : -2.27 (0.15), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 63 TYR 0.015 0.001 TYR K 51 PHE 0.017 0.002 PHE H 29 TRP 0.031 0.002 TRP D 571 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00465 (20622) covalent geometry : angle 0.65182 (28020) SS BOND : bond 0.00466 ( 36) SS BOND : angle 1.11223 ( 72) hydrogen bonds : bond 0.03528 ( 604) hydrogen bonds : angle 4.68231 ( 1674) link_ALPHA1-2 : bond 0.00645 ( 3) link_ALPHA1-2 : angle 2.16079 ( 9) link_ALPHA1-3 : bond 0.00942 ( 9) link_ALPHA1-3 : angle 2.01913 ( 27) link_ALPHA1-6 : bond 0.00641 ( 9) link_ALPHA1-6 : angle 1.54871 ( 27) link_BETA1-4 : bond 0.00551 ( 24) link_BETA1-4 : angle 1.60126 ( 72) link_NAG-ASN : bond 0.00435 ( 42) link_NAG-ASN : angle 3.05257 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 350 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8443 (tp) cc_final: 0.8087 (tt) REVERT: A 377 ASN cc_start: 0.8836 (t0) cc_final: 0.8585 (t0) REVERT: A 425 ASN cc_start: 0.7953 (t0) cc_final: 0.7565 (t0) REVERT: B 99 ASP cc_start: 0.7425 (t70) cc_final: 0.6902 (t0) REVERT: B 180 ASP cc_start: 0.8861 (m-30) cc_final: 0.8358 (t0) REVERT: D 538 THR cc_start: 0.9176 (p) cc_final: 0.8899 (t) REVERT: F 589 ASP cc_start: 0.8344 (t0) cc_final: 0.8012 (t0) REVERT: F 632 ASP cc_start: 0.8677 (t0) cc_final: 0.8401 (t0) REVERT: I 12 LYS cc_start: 0.8630 (mmmm) cc_final: 0.8209 (mmmm) REVERT: I 23 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7833 (tppt) REVERT: I 91 THR cc_start: 0.7993 (p) cc_final: 0.7733 (p) outliers start: 70 outliers final: 59 residues processed: 393 average time/residue: 0.1339 time to fit residues: 83.6161 Evaluate side-chains 395 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 335 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 105 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 138 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.140747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110330 restraints weight = 32817.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110729 restraints weight = 29004.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111695 restraints weight = 25784.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112120 restraints weight = 21548.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112536 restraints weight = 20434.378| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20745 Z= 0.144 Angle : 0.651 9.180 28353 Z= 0.314 Chirality : 0.046 0.346 3384 Planarity : 0.004 0.065 3456 Dihedral : 10.467 111.906 4413 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.25 % Allowed : 18.06 % Favored : 78.69 % 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 aren not related in a simple way. whole: -1.54 (0.17), residues: 2427 helix: 1.22 (0.29), residues: 366 sheet: -0.19 (0.21), residues: 654 loop : -2.17 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 72 TYR 0.015 0.001 TYR E 638 PHE 0.017 0.001 PHE H 29 TRP 0.037 0.002 TRP H 36 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00340 (20622) covalent geometry : angle 0.61404 (28020) SS BOND : bond 0.00453 ( 36) SS BOND : angle 1.05153 ( 72) hydrogen bonds : bond 0.03203 ( 604) hydrogen bonds : angle 4.56330 ( 1674) link_ALPHA1-2 : bond 0.00955 ( 3) link_ALPHA1-2 : angle 2.22059 ( 9) link_ALPHA1-3 : bond 0.00982 ( 9) link_ALPHA1-3 : angle 1.85072 ( 27) link_ALPHA1-6 : bond 0.00820 ( 9) link_ALPHA1-6 : angle 1.38074 ( 27) link_BETA1-4 : bond 0.00520 ( 24) link_BETA1-4 : angle 1.52363 ( 72) link_NAG-ASN : bond 0.00391 ( 42) link_NAG-ASN : angle 2.85045 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 349 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8435 (tp) cc_final: 0.8065 (tt) REVERT: A 377 ASN cc_start: 0.8837 (t0) cc_final: 0.8513 (t0) REVERT: A 425 ASN cc_start: 0.8026 (t0) cc_final: 0.7705 (t0) REVERT: B 99 ASP cc_start: 0.7389 (t70) cc_final: 0.6876 (t0) REVERT: B 180 ASP cc_start: 0.8859 (m-30) cc_final: 0.8383 (t0) REVERT: C 104 MET cc_start: 0.8815 (tpt) cc_final: 0.8438 (tpp) REVERT: C 154 MET cc_start: 0.8819 (mtt) cc_final: 0.8443 (mtt) REVERT: C 301 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7760 (m110) REVERT: D 538 THR cc_start: 0.9147 (p) cc_final: 0.8864 (t) REVERT: D 596 TRP cc_start: 0.7958 (p90) cc_final: 0.7639 (p90) REVERT: D 630 GLN cc_start: 0.7955 (pm20) cc_final: 0.7742 (pm20) REVERT: F 589 ASP cc_start: 0.8346 (t0) cc_final: 0.8023 (t0) REVERT: F 632 ASP cc_start: 0.8689 (t0) cc_final: 0.8487 (t0) REVERT: I 12 LYS cc_start: 0.8598 (mmmm) cc_final: 0.8230 (mmmm) REVERT: I 23 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7849 (tppt) REVERT: L 68 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7972 (ttpt) outliers start: 69 outliers final: 50 residues processed: 392 average time/residue: 0.1284 time to fit residues: 79.2002 Evaluate side-chains 391 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 546 SER Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain K residue 67 SER Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 84 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 67 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 219 optimal weight: 0.5980 chunk 206 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.141104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111364 restraints weight = 32540.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112153 restraints weight = 29088.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112830 restraints weight = 25764.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113280 restraints weight = 21649.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113398 restraints weight = 20708.736| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 20745 Z= 0.135 Angle : 0.648 9.110 28353 Z= 0.314 Chirality : 0.045 0.345 3384 Planarity : 0.004 0.062 3456 Dihedral : 10.056 110.683 4413 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.83 % Allowed : 18.86 % Favored : 78.31 % 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 aren not related in a simple way. whole: -1.47 (0.17), residues: 2427 helix: 1.30 (0.29), residues: 366 sheet: -0.07 (0.21), residues: 624 loop : -2.14 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.016 0.001 TYR L 38 PHE 0.019 0.001 PHE H 29 TRP 0.039 0.002 TRP H 36 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00319 (20622) covalent geometry : angle 0.61346 (28020) SS BOND : bond 0.00437 ( 36) SS BOND : angle 1.12078 ( 72) hydrogen bonds : bond 0.03091 ( 604) hydrogen bonds : angle 4.54327 ( 1674) link_ALPHA1-2 : bond 0.00958 ( 3) link_ALPHA1-2 : angle 2.30602 ( 9) link_ALPHA1-3 : bond 0.00980 ( 9) link_ALPHA1-3 : angle 1.77459 ( 27) link_ALPHA1-6 : bond 0.00856 ( 9) link_ALPHA1-6 : angle 1.38382 ( 27) link_BETA1-4 : bond 0.00535 ( 24) link_BETA1-4 : angle 1.46899 ( 72) link_NAG-ASN : bond 0.00393 ( 42) link_NAG-ASN : angle 2.73604 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 347 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8400 (tp) cc_final: 0.8050 (tt) REVERT: B 99 ASP cc_start: 0.7332 (t70) cc_final: 0.6832 (t0) REVERT: B 180 ASP cc_start: 0.8847 (m-30) cc_final: 0.8444 (t0) REVERT: C 104 MET cc_start: 0.8872 (tpt) cc_final: 0.8421 (tpp) REVERT: C 154 MET cc_start: 0.8821 (mtt) cc_final: 0.8510 (mtt) REVERT: D 596 TRP cc_start: 0.7913 (p90) cc_final: 0.7575 (p90) REVERT: D 624 ASP cc_start: 0.7485 (m-30) cc_final: 0.7246 (p0) REVERT: F 589 ASP cc_start: 0.8216 (t0) cc_final: 0.7879 (t0) REVERT: I 12 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8227 (mmmm) REVERT: I 23 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7806 (tppt) outliers start: 60 outliers final: 54 residues processed: 384 average time/residue: 0.1393 time to fit residues: 84.4949 Evaluate side-chains 390 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 335 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 135 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 189 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107167 restraints weight = 32719.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107632 restraints weight = 29569.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108254 restraints weight = 27787.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108734 restraints weight = 23319.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108906 restraints weight = 21804.572| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20745 Z= 0.219 Angle : 0.730 9.347 28353 Z= 0.354 Chirality : 0.047 0.347 3384 Planarity : 0.004 0.057 3456 Dihedral : 10.247 113.698 4413 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.52 % Favored : 90.44 % Rotamer: Outliers : 3.16 % Allowed : 18.91 % Favored : 77.93 % 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 aren not related in a simple way. whole: -1.62 (0.17), residues: 2427 helix: 0.85 (0.29), residues: 384 sheet: -0.08 (0.21), residues: 648 loop : -2.26 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 72 TYR 0.016 0.002 TYR A 191 PHE 0.021 0.002 PHE H 29 TRP 0.049 0.002 TRP F 571 HIS 0.007 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00519 (20622) covalent geometry : angle 0.69172 (28020) SS BOND : bond 0.00507 ( 36) SS BOND : angle 1.31679 ( 72) hydrogen bonds : bond 0.03743 ( 604) hydrogen bonds : angle 4.76994 ( 1674) link_ALPHA1-2 : bond 0.00592 ( 3) link_ALPHA1-2 : angle 2.48421 ( 9) link_ALPHA1-3 : bond 0.00956 ( 9) link_ALPHA1-3 : angle 1.93270 ( 27) link_ALPHA1-6 : bond 0.00714 ( 9) link_ALPHA1-6 : angle 1.41242 ( 27) link_BETA1-4 : bond 0.00595 ( 24) link_BETA1-4 : angle 1.63175 ( 72) link_NAG-ASN : bond 0.00477 ( 42) link_NAG-ASN : angle 3.04459 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 337 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8516 (tp) cc_final: 0.8156 (tt) REVERT: B 180 ASP cc_start: 0.8912 (m-30) cc_final: 0.8402 (t0) REVERT: C 104 MET cc_start: 0.8892 (tpt) cc_final: 0.8218 (tpt) REVERT: D 522 PHE cc_start: 0.6213 (OUTLIER) cc_final: 0.5117 (m-80) REVERT: D 538 THR cc_start: 0.9099 (p) cc_final: 0.8879 (t) REVERT: D 624 ASP cc_start: 0.7453 (m-30) cc_final: 0.7158 (p0) REVERT: H 78 THR cc_start: 0.8090 (m) cc_final: 0.7774 (p) REVERT: I 12 LYS cc_start: 0.8632 (mmmm) cc_final: 0.8339 (mmmm) REVERT: I 23 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7895 (tppt) outliers start: 67 outliers final: 53 residues processed: 381 average time/residue: 0.1345 time to fit residues: 80.9092 Evaluate side-chains 384 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 329 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 117 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109360 restraints weight = 32675.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109807 restraints weight = 29030.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110241 restraints weight = 27852.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110854 restraints weight = 23540.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111121 restraints weight = 21792.578| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 20745 Z= 0.160 Angle : 0.688 9.141 28353 Z= 0.333 Chirality : 0.046 0.342 3384 Planarity : 0.004 0.057 3456 Dihedral : 9.891 110.160 4413 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.41 % Favored : 91.51 % Rotamer: Outliers : 3.02 % Allowed : 19.24 % Favored : 77.75 % 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 aren not related in a simple way. whole: -1.49 (0.17), residues: 2427 helix: 1.25 (0.29), residues: 366 sheet: -0.13 (0.21), residues: 663 loop : -2.17 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 72 TYR 0.020 0.001 TYR L 89 PHE 0.020 0.002 PHE H 29 TRP 0.047 0.002 TRP F 571 HIS 0.005 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00382 (20622) covalent geometry : angle 0.65208 (28020) SS BOND : bond 0.00469 ( 36) SS BOND : angle 1.21324 ( 72) hydrogen bonds : bond 0.03370 ( 604) hydrogen bonds : angle 4.65929 ( 1674) link_ALPHA1-2 : bond 0.00967 ( 3) link_ALPHA1-2 : angle 2.50915 ( 9) link_ALPHA1-3 : bond 0.00940 ( 9) link_ALPHA1-3 : angle 1.67165 ( 27) link_ALPHA1-6 : bond 0.00838 ( 9) link_ALPHA1-6 : angle 1.27254 ( 27) link_BETA1-4 : bond 0.00559 ( 24) link_BETA1-4 : angle 1.57990 ( 72) link_NAG-ASN : bond 0.00399 ( 42) link_NAG-ASN : angle 2.89606 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4854 Ramachandran restraints generated. 2427 Oldfield, 0 Emsley, 2427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 344 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8462 (tp) cc_final: 0.8087 (tt) REVERT: B 99 ASP cc_start: 0.7338 (t70) cc_final: 0.6905 (t0) REVERT: B 180 ASP cc_start: 0.8874 (m-30) cc_final: 0.8433 (t0) REVERT: C 104 MET cc_start: 0.8876 (tpt) cc_final: 0.8141 (tpt) REVERT: C 475 MET cc_start: 0.8447 (tpt) cc_final: 0.8038 (tpp) REVERT: D 538 THR cc_start: 0.9181 (p) cc_final: 0.8920 (t) REVERT: D 596 TRP cc_start: 0.7961 (p90) cc_final: 0.7604 (p90) REVERT: D 624 ASP cc_start: 0.7457 (m-30) cc_final: 0.7187 (p0) REVERT: E 596 TRP cc_start: 0.7623 (p90) cc_final: 0.7301 (p90) REVERT: F 589 ASP cc_start: 0.8217 (t0) cc_final: 0.7900 (t0) REVERT: H 78 THR cc_start: 0.8114 (m) cc_final: 0.7767 (p) REVERT: I 12 LYS cc_start: 0.8667 (mmmm) cc_final: 0.8363 (mmmm) REVERT: I 23 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7890 (tppt) outliers start: 64 outliers final: 56 residues processed: 384 average time/residue: 0.1380 time to fit residues: 83.5585 Evaluate side-chains 393 residues out of total 2121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 336 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 CYS Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain E residue 522 PHE Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 627 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 23 LYS Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain L residue 18 ILE Chi-restraints excluded: chain L residue 25 THR Chi-restraints excluded: chain L residue 77 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 197 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 156 optimal weight: 0.2980 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108941 restraints weight = 32617.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109681 restraints weight = 28660.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110445 restraints weight = 25452.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110943 restraints weight = 21920.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111356 restraints weight = 20326.487| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 20745 Z= 0.150 Angle : 0.678 9.667 28353 Z= 0.327 Chirality : 0.046 0.337 3384 Planarity : 0.004 0.052 3456 Dihedral : 9.613 108.921 4413 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.36 % Favored : 91.55 % Rotamer: Outliers : 2.78 % Allowed : 19.80 % Favored : 77.42 % 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 aren not related in a simple way. whole: -1.47 (0.17), residues: 2427 helix: 1.27 (0.29), residues: 366 sheet: -0.14 (0.21), residues: 663 loop : -2.14 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 38 TYR 0.017 0.001 TYR L 89 PHE 0.019 0.002 PHE H 29 TRP 0.046 0.002 TRP F 571 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00358 (20622) covalent geometry : angle 0.64290 (28020) SS BOND : bond 0.00455 ( 36) SS BOND : angle 1.16199 ( 72) hydrogen bonds : bond 0.03234 ( 604) hydrogen bonds : angle 4.59831 ( 1674) link_ALPHA1-2 : bond 0.01012 ( 3) link_ALPHA1-2 : angle 2.64037 ( 9) link_ALPHA1-3 : bond 0.00876 ( 9) link_ALPHA1-3 : angle 1.62217 ( 27) link_ALPHA1-6 : bond 0.00836 ( 9) link_ALPHA1-6 : angle 1.27772 ( 27) link_BETA1-4 : bond 0.00560 ( 24) link_BETA1-4 : angle 1.52842 ( 72) link_NAG-ASN : bond 0.00407 ( 42) link_NAG-ASN : angle 2.81047 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.00 seconds wall clock time: 53 minutes 8.22 seconds (3188.22 seconds total)