Starting phenix.real_space_refine on Fri Sep 19 05:34:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.map" model { file = "/net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cu6_45929/09_2025/9cu6_45929.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.025 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 149 5.16 5 C 14848 2.51 5 N 3966 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 23631 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4529 Classifications: {'peptide': 569} Link IDs: {'PTRANS': 23, 'TRANS': 545} Chain breaks: 6 Chain: "D" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 962 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "E" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "F" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "J" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1009 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 851 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "B" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4466 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 6 Chain: "I" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 962 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 116} Chain: "M" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 4463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 4463 Classifications: {'peptide': 561} Link IDs: {'PTRANS': 23, 'TRANS': 537} Chain breaks: 5 Chain: "N" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 5.06, per 1000 atoms: 0.21 Number of scatterers: 23631 At special positions: 0 Unit cell: (159.498, 138.784, 133.605, 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 149 16.00 O 4668 8.00 N 3966 7.00 C 14848 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 662 " distance=2.03 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS C 501 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=1.82 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 89 " - pdb=" SG CYS G 96 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 96 " 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=2.04 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 196 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 157 " distance=2.03 Simple disulfide: pdb=" SG CYS B 218 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 331 " distance=2.02 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 445 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 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 P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA R 3 " - " MAN R 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " BETA1-6 " NAG Q 1 " - " FUC Q 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG V 1 " - " FUC V 3 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 241 " " NAG A 703 " - " ASN A 276 " " NAG A 704 " - " ASN A 295 " " NAG A 705 " - " ASN A 301 " " NAG A 706 " - " ASN A 332 " " NAG A 707 " - " ASN A 362 " " NAG A 708 " - " ASN A 386 " " NAG A 709 " - " ASN A 392 " " NAG A 710 " - " ASN A 448 " " NAG A 711 " - " ASN A 339 " " NAG B 701 " - " ASN B 160 " " NAG B 702 " - " ASN B 276 " " NAG B 703 " - " ASN B 295 " " NAG B 704 " - " ASN B 301 " " NAG B 705 " - " ASN B 332 " " NAG B 706 " - " ASN B 362 " " NAG B 707 " - " ASN B 386 " " NAG B 708 " - " ASN B 392 " " NAG B 709 " - " ASN B 448 " " NAG B 710 " - " ASN B 339 " " NAG B 711 " - " ASN B 637 " " NAG C 701 " - " ASN C 160 " " NAG C 702 " - " ASN C 241 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 301 " " NAG C 706 " - " ASN C 332 " " NAG C 707 " - " ASN C 362 " " NAG C 708 " - " ASN C 386 " " NAG C 709 " - " ASN C 392 " " NAG C 710 " - " ASN C 448 " " NAG C 711 " - " ASN C 339 " " NAG C 712 " - " ASN C 625 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 625 " " NAG R 1 " - " ASN B 88 " " NAG S 1 " - " ASN B 156 " " NAG T 1 " - " ASN B 241 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN B 625 " " NAG W 1 " - " ASN C 88 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 262 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 712.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5310 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 44 sheets defined 18.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.010A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.503A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.515A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG 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 484 removed outlier: 3.735A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 536 through 542 removed outlier: 3.978A pdb=" N GLN A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 597 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 651 Processing helix chain 'A' and resid 653 through 662 removed outlier: 3.559A pdb=" N GLU A 659 " --> pdb=" O LYS A 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'E' and resid 26 through 27C Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.542A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 26 through 27C Processing helix chain 'G' and resid 79 through 84 removed outlier: 4.018A pdb=" N THR G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.580A pdb=" N TYR J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'K' and resid 26 through 27C Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.071A pdb=" N GLU B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 3.951A pdb=" N GLN B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.527A pdb=" N GLY B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 381 " --> pdb=" O CYS B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 475 through 484 removed outlier: 3.596A pdb=" N TRP B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B 482 " --> pdb=" O ASN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.894A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 649 removed outlier: 3.511A pdb=" N THR B 644 " --> pdb=" O SER B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.600A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 65 removed outlier: 4.638A pdb=" N ASN I 65 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.861A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.604A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.766A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 536 through 542 removed outlier: 3.694A pdb=" N GLN C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 597 removed outlier: 3.588A pdb=" N LYS C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.532A pdb=" N ASN C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 635 through 649 removed outlier: 4.659A pdb=" N SER C 640 " --> pdb=" O ASP C 636 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLU C 641 " --> pdb=" O ASN C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 655 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.148A pdb=" N VAL A 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL A 38 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR A 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N TYR A 40 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS A 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.700A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 168 through 177 removed outlier: 4.289A pdb=" N LYS A 168 " --> pdb=" O THR A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.543A pdb=" N ALA A 433 " --> pdb=" O VAL A 200 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 298 removed outlier: 7.131A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 330 through 334 current: chain 'A' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 383 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.956A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 27 current: chain 'D' and resid 74 through 82 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 10 through 12 current: chain 'D' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 57 through 59 current: chain 'D' and resid 100F through 103 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100F through 103 Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'E' and resid 11 through 14 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 11 through 14 current: chain 'E' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 45 through 48 current: chain 'E' and resid 97 through 98 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 5 through 6 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 27 current: chain 'F' and resid 73 through 82 Processing sheet with id=AB7, first strand: chain 'F' and resid 34 through 40 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 45 current: chain 'F' and resid 57 through 59 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 57 through 59 current: chain 'F' and resid 100F through 103 Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.758A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER L 67 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.402A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AC2, first strand: chain 'G' and resid 9 through 14 removed outlier: 5.257A pdb=" N GLY G 95A" --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR G 92 " --> pdb=" O GLY G 95A" (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS G 88 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR G 86 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ILE G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N TYR G 49 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP G 35 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 18 through 27 current: chain 'J' and resid 74 through 82 Processing sheet with id=AC4, first strand: chain 'J' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 10 through 12 current: chain 'J' and resid 44 through 51 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100F through 103 Processing sheet with id=AC5, first strand: chain 'K' and resid 9 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 9 through 14 current: chain 'K' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 45 through 48 current: chain 'K' and resid 96 through 98 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AC7, first strand: chain 'B' and resid 494 through 499 removed outlier: 4.819A pdb=" N VAL B 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 45 through 47 removed outlier: 3.887A pdb=" N ILE B 225 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL B 242 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.714A pdb=" N CYS B 54 " --> pdb=" O VAL B 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 91 through 94 Processing sheet with id=AD2, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.419A pdb=" N ILE B 201 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B 202 " --> pdb=" O TYR B 435 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 170 through 177 Processing sheet with id=AD4, first strand: chain 'B' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 259 through 261 current: chain 'B' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 284 through 287 current: chain 'B' and resid 330 through 334 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 330 through 334 current: chain 'B' and resid 383 through 385 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 383 through 385 current: chain 'B' and resid 465 through 470 No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 304 through 312 removed outlier: 7.009A pdb=" N ARG B 315 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 7 removed outlier: 6.621A pdb=" N GLN I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 100F through 103 Processing sheet with id=AD8, first strand: chain 'M' and resid 4 through 7 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 19 through 25 current: chain 'M' and resid 70 through 75 Processing sheet with id=AD9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.348A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.971A pdb=" N VAL C 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.633A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.950A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AE5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AE6, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.928A pdb=" N ALA C 433 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 298 removed outlier: 7.274A pdb=" N GLU C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER C 334 " --> pdb=" O GLU C 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 330 through 334 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AE8, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.203A pdb=" N ASN C 301 " --> pdb=" O ILE C 322 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE C 322 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 321 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7130 1.34 - 1.47: 6398 1.47 - 1.59: 10420 1.59 - 1.72: 0 1.72 - 1.85: 201 Bond restraints: 24149 Sorted by residual: bond pdb=" CA TYR I 100D" pdb=" C TYR I 100D" ideal model delta sigma weight residual 1.523 1.476 0.047 1.35e-02 5.49e+03 1.21e+01 bond pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.02e-02 9.61e+03 1.11e+01 bond pdb=" N ILE K 48 " pdb=" CA ILE K 48 " ideal model delta sigma weight residual 1.464 1.501 -0.038 1.13e-02 7.83e+03 1.10e+01 bond pdb=" N SER G 90 " pdb=" CA SER G 90 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N ILE D 51 " pdb=" CA ILE D 51 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.98e+00 ... (remaining 24144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 31721 2.86 - 5.72: 961 5.72 - 8.58: 98 8.58 - 11.44: 11 11.44 - 14.30: 2 Bond angle restraints: 32793 Sorted by residual: angle pdb=" C GLN A 650 " pdb=" N ASN A 651 " pdb=" CA ASN A 651 " ideal model delta sigma weight residual 122.24 108.89 13.35 1.57e+00 4.06e-01 7.23e+01 angle pdb=" C SER A 649 " pdb=" N GLN A 650 " pdb=" CA GLN A 650 " ideal model delta sigma weight residual 122.42 108.12 14.30 1.77e+00 3.19e-01 6.53e+01 angle pdb=" N TYR H 100D" pdb=" CA TYR H 100D" pdb=" C TYR H 100D" ideal model delta sigma weight residual 113.12 103.83 9.29 1.25e+00 6.40e-01 5.52e+01 angle pdb=" N TYR I 100D" pdb=" CA TYR I 100D" pdb=" CB TYR I 100D" ideal model delta sigma weight residual 110.28 119.95 -9.67 1.55e+00 4.16e-01 3.89e+01 angle pdb=" C GLU K 50 " pdb=" N ASP K 51 " pdb=" CA ASP K 51 " ideal model delta sigma weight residual 120.71 110.84 9.87 1.67e+00 3.59e-01 3.49e+01 ... (remaining 32788 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 14433 22.41 - 44.82: 727 44.82 - 67.22: 167 67.22 - 89.63: 62 89.63 - 112.04: 24 Dihedral angle restraints: 15413 sinusoidal: 7143 harmonic: 8270 Sorted by residual: dihedral pdb=" CB CYS K 89 " pdb=" SG CYS K 89 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual -86.00 -170.53 84.53 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 25.62 67.38 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS E 89 " pdb=" SG CYS E 89 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 38.01 54.99 1 1.00e+01 1.00e-02 4.09e+01 ... (remaining 15410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 3811 0.187 - 0.374: 36 0.374 - 0.561: 1 0.561 - 0.748: 0 0.748 - 0.936: 3 Chirality restraints: 3851 Sorted by residual: chirality pdb=" C1 NAG B 710 " pdb=" ND2 ASN B 339 " pdb=" C2 NAG B 710 " pdb=" O5 NAG B 710 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.19e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 156 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 262 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 3848 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER M 14 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C SER M 14 " -0.069 2.00e-02 2.50e+03 pdb=" O SER M 14 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL M 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 49 " -0.034 2.00e-02 2.50e+03 2.75e-02 1.51e+01 pdb=" CG TYR M 49 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR M 49 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR M 49 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR M 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR M 49 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR M 49 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 49 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 636 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.38e+01 pdb=" C ASP C 636 " 0.064 2.00e-02 2.50e+03 pdb=" O ASP C 636 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN C 637 " -0.022 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 791 2.70 - 3.25: 22397 3.25 - 3.80: 36849 3.80 - 4.35: 49012 4.35 - 4.90: 81228 Nonbonded interactions: 190277 Sorted by model distance: nonbonded pdb=" CG ARG A 503 " pdb=" O THR A 605 " model vdw 2.144 3.440 nonbonded pdb=" OH TYR J 53 " pdb=" OE1 GLU B 87 " model vdw 2.155 3.040 nonbonded pdb=" NE2 GLN A 652 " pdb=" O SER C 534 " model vdw 2.177 3.120 nonbonded pdb=" O GLU B 641 " pdb=" OG1 THR B 644 " model vdw 2.195 3.040 nonbonded pdb=" OD1 ASP K 82 " pdb=" OH TYR K 86 " model vdw 2.207 3.040 ... (remaining 190272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 59 or resid 64 through 136 or resid 150 through \ 503 or resid 521 through 655 or resid 701 through 711)) selection = (chain 'B' and (resid 32 through 503 or resid 521 through 655 or resid 701 throu \ gh 711)) selection = (chain 'C' and (resid 32 through 59 or resid 64 through 136 or resid 150 through \ 503 or resid 521 through 655 or resid 702 through 712)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'X' } ncs_group { reference = chain 'Q' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.680 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 : 0.007 0.207 24271 Z= 0.306 Angle : 1.188 35.520 33114 Z= 0.630 Chirality : 0.067 0.936 3851 Planarity : 0.006 0.088 4064 Dihedral : 14.817 112.039 9968 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.20 % Allowed : 10.96 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.59 (0.15), residues: 2814 helix: 0.68 (0.26), residues: 356 sheet: 0.80 (0.16), residues: 970 loop : 0.15 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 440 TYR 0.068 0.004 TYR M 49 PHE 0.044 0.004 PHE L 98 TRP 0.052 0.003 TRP J 36 HIS 0.010 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00634 (24149) covalent geometry : angle 1.13002 (32793) SS BOND : bond 0.03747 ( 45) SS BOND : angle 4.92631 ( 90) hydrogen bonds : bond 0.16626 ( 616) hydrogen bonds : angle 7.57347 ( 1596) link_ALPHA1-2 : bond 0.00149 ( 2) link_ALPHA1-2 : angle 1.74694 ( 6) link_ALPHA1-3 : bond 0.00319 ( 6) link_ALPHA1-3 : angle 2.61480 ( 18) link_ALPHA1-6 : bond 0.00759 ( 3) link_ALPHA1-6 : angle 2.58523 ( 9) link_BETA1-4 : bond 0.01441 ( 18) link_BETA1-4 : angle 4.23731 ( 54) link_BETA1-6 : bond 0.00716 ( 2) link_BETA1-6 : angle 2.53908 ( 6) link_NAG-ASN : bond 0.00474 ( 46) link_NAG-ASN : angle 3.30329 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 568 time to evaluate : 0.789 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 57 ASP cc_start: 0.7969 (t0) cc_final: 0.7644 (t0) REVERT: A 164 GLU cc_start: 0.5746 (tp30) cc_final: 0.5468 (tp30) REVERT: A 327 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7675 (mtp85) REVERT: A 535 MET cc_start: 0.8678 (mpp) cc_final: 0.8464 (mpp) REVERT: A 616 ASN cc_start: 0.8695 (p0) cc_final: 0.8370 (p0) REVERT: A 632 GLU cc_start: 0.8626 (tp30) cc_final: 0.8354 (tp30) REVERT: A 655 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8700 (mmmm) REVERT: D 3 GLN cc_start: 0.6683 (tm-30) cc_final: 0.6471 (tm-30) REVERT: D 19 LYS cc_start: 0.8399 (tttm) cc_final: 0.8100 (tttm) REVERT: D 31 PHE cc_start: 0.9003 (m-10) cc_final: 0.8773 (m-10) REVERT: D 39 GLN cc_start: 0.7502 (tp40) cc_final: 0.7249 (tp40) REVERT: D 58 ASN cc_start: 0.8137 (t0) cc_final: 0.7903 (t0) REVERT: D 79 TYR cc_start: 0.7910 (m-80) cc_final: 0.7483 (m-10) REVERT: D 82 ASN cc_start: 0.8100 (m-40) cc_final: 0.7888 (m110) REVERT: H 5 GLN cc_start: 0.8954 (tp40) cc_final: 0.8729 (tp40) REVERT: H 13 ARG cc_start: 0.7794 (mtt-85) cc_final: 0.7519 (mtt-85) REVERT: E 35 TRP cc_start: 0.8210 (m100) cc_final: 0.7676 (m100) REVERT: F 83 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7106 (mptt) REVERT: L 83 PHE cc_start: 0.8628 (t80) cc_final: 0.8345 (t80) REVERT: G 42 ARG cc_start: 0.8448 (ttm110) cc_final: 0.7883 (mtp85) REVERT: G 66 LYS cc_start: 0.8367 (ttpp) cc_final: 0.8105 (ttpp) REVERT: G 68 TYR cc_start: 0.7963 (m-80) cc_final: 0.7336 (t80) REVERT: J 57 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8433 (mtpt) REVERT: J 58 ASN cc_start: 0.8161 (m-40) cc_final: 0.7826 (m-40) REVERT: J 80 MET cc_start: 0.7691 (ttt) cc_final: 0.7298 (ttm) REVERT: J 90 TYR cc_start: 0.7890 (m-80) cc_final: 0.7523 (m-80) REVERT: K 29 SER cc_start: 0.8624 (t) cc_final: 0.8345 (p) REVERT: K 53 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6847 (mp0) REVERT: K 72 TYR cc_start: 0.6518 (m-10) cc_final: 0.6310 (m-10) REVERT: B 35 TRP cc_start: 0.8339 (m100) cc_final: 0.7984 (m100) REVERT: B 110 SER cc_start: 0.8975 (t) cc_final: 0.8368 (m) REVERT: B 160 ASN cc_start: 0.8130 (m-40) cc_final: 0.7718 (p0) REVERT: B 189 THR cc_start: 0.9044 (p) cc_final: 0.8517 (t) REVERT: B 327 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7508 (mmp80) REVERT: B 446 SER cc_start: 0.9143 (t) cc_final: 0.8646 (p) REVERT: B 475 MET cc_start: 0.8784 (mmm) cc_final: 0.8506 (tpp) REVERT: B 579 ARG cc_start: 0.8221 (mtp85) cc_final: 0.8002 (mtm180) REVERT: I 53 TYR cc_start: 0.9333 (t80) cc_final: 0.9018 (t80) REVERT: M 36 TYR cc_start: 0.8739 (m-10) cc_final: 0.8482 (m-80) REVERT: M 42 LYS cc_start: 0.8043 (mmmm) cc_final: 0.7778 (mmmt) REVERT: M 79 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8652 (mm110) REVERT: C 35 TRP cc_start: 0.8417 (m100) cc_final: 0.8199 (m100) REVERT: C 37 THR cc_start: 0.9147 (m) cc_final: 0.8825 (p) REVERT: C 46 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7880 (mttm) REVERT: C 53 PHE cc_start: 0.7590 (p90) cc_final: 0.7370 (p90) REVERT: C 168 LYS cc_start: 0.8626 (ttmm) cc_final: 0.8090 (mmtm) REVERT: C 217 TYR cc_start: 0.7943 (m-80) cc_final: 0.7670 (m-80) REVERT: C 355 ASN cc_start: 0.6765 (m-40) cc_final: 0.5842 (p0) REVERT: C 492 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 634 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7725 (mm-30) outliers start: 5 outliers final: 2 residues processed: 573 average time/residue: 0.1719 time to fit residues: 147.2573 Evaluate side-chains 483 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 481 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 650 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.0770 chunk 111 optimal weight: 3.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN L 34 ASN J 105 GLN B 249 HIS B 363 HIS B 422 GLN B 624 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN C 66 HIS C 246 GLN C 249 HIS C 575 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.132836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104953 restraints weight = 38891.347| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.07 r_work: 0.3267 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24271 Z= 0.161 Angle : 0.705 14.495 33114 Z= 0.353 Chirality : 0.048 0.492 3851 Planarity : 0.004 0.037 4064 Dihedral : 9.702 81.584 4684 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.35 % Allowed : 11.27 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.51 (0.15), residues: 2814 helix: 1.16 (0.27), residues: 360 sheet: 0.71 (0.15), residues: 1004 loop : -0.06 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 503 TYR 0.032 0.002 TYR G 49 PHE 0.016 0.002 PHE C 277 TRP 0.022 0.002 TRP D 50 HIS 0.004 0.001 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00364 (24149) covalent geometry : angle 0.66958 (32793) SS BOND : bond 0.00561 ( 45) SS BOND : angle 1.50305 ( 90) hydrogen bonds : bond 0.04553 ( 616) hydrogen bonds : angle 6.08380 ( 1596) link_ALPHA1-2 : bond 0.00126 ( 2) link_ALPHA1-2 : angle 1.97710 ( 6) link_ALPHA1-3 : bond 0.00609 ( 6) link_ALPHA1-3 : angle 2.07410 ( 18) link_ALPHA1-6 : bond 0.01075 ( 3) link_ALPHA1-6 : angle 2.14427 ( 9) link_BETA1-4 : bond 0.00828 ( 18) link_BETA1-4 : angle 2.79713 ( 54) link_BETA1-6 : bond 0.00499 ( 2) link_BETA1-6 : angle 2.08316 ( 6) link_NAG-ASN : bond 0.00377 ( 46) link_NAG-ASN : angle 2.63450 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 515 time to evaluate : 0.873 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 57 ASP cc_start: 0.7979 (t0) cc_final: 0.7613 (t0) REVERT: A 616 ASN cc_start: 0.8745 (p0) cc_final: 0.8381 (p0) REVERT: A 632 GLU cc_start: 0.8765 (tp30) cc_final: 0.8471 (tp30) REVERT: A 652 GLN cc_start: 0.8758 (tp40) cc_final: 0.8553 (tp40) REVERT: D 58 ASN cc_start: 0.8165 (t0) cc_final: 0.7894 (t0) REVERT: D 79 TYR cc_start: 0.8214 (m-80) cc_final: 0.7888 (m-10) REVERT: D 80 MET cc_start: 0.8161 (tmm) cc_final: 0.7736 (tmm) REVERT: D 82 ASN cc_start: 0.8093 (m-40) cc_final: 0.7835 (m110) REVERT: H 81 LYS cc_start: 0.8990 (mmtt) cc_final: 0.8759 (mmmm) REVERT: F 19 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7043 (ttmm) REVERT: F 57 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8272 (mttt) REVERT: F 59 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7897 (tp) REVERT: F 66 ARG cc_start: 0.6357 (ttm170) cc_final: 0.5540 (ttt180) REVERT: F 82 ARG cc_start: 0.7028 (mtp180) cc_final: 0.6770 (mtp-110) REVERT: F 82 LEU cc_start: 0.8303 (mp) cc_final: 0.8003 (mp) REVERT: F 83 LYS cc_start: 0.8090 (mmtm) cc_final: 0.7435 (mptt) REVERT: L 4 MET cc_start: 0.8753 (mmm) cc_final: 0.8397 (mmm) REVERT: G 12 SER cc_start: 0.8737 (t) cc_final: 0.8532 (m) REVERT: G 42 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7838 (mtp-110) REVERT: G 54 ARG cc_start: 0.8476 (mtm180) cc_final: 0.7971 (mtp180) REVERT: J 19 LYS cc_start: 0.8230 (tptt) cc_final: 0.7026 (tptp) REVERT: J 46 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7744 (tm-30) REVERT: J 58 ASN cc_start: 0.8224 (m-40) cc_final: 0.7872 (m-40) REVERT: J 80 MET cc_start: 0.7668 (ttt) cc_final: 0.7407 (ttm) REVERT: J 90 TYR cc_start: 0.7779 (m-80) cc_final: 0.7326 (m-80) REVERT: J 105 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: K 17 GLN cc_start: 0.7417 (tt0) cc_final: 0.7127 (pt0) REVERT: K 29 SER cc_start: 0.8570 (t) cc_final: 0.8263 (p) REVERT: K 42 ARG cc_start: 0.7456 (mtm-85) cc_final: 0.7096 (mtm-85) REVERT: B 35 TRP cc_start: 0.8345 (m100) cc_final: 0.7675 (m-90) REVERT: B 110 SER cc_start: 0.9118 (t) cc_final: 0.8518 (m) REVERT: B 126 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7311 (t) REVERT: B 160 ASN cc_start: 0.8287 (m-40) cc_final: 0.7713 (p0) REVERT: B 327 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7745 (mmp80) REVERT: B 446 SER cc_start: 0.9120 (t) cc_final: 0.8610 (p) REVERT: B 490 LYS cc_start: 0.8887 (tttm) cc_final: 0.8577 (tttp) REVERT: B 579 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7997 (mtm180) REVERT: M 48 ILE cc_start: 0.9611 (mm) cc_final: 0.9389 (mm) REVERT: M 79 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8461 (mm110) REVERT: C 91 GLU cc_start: 0.8313 (tp30) cc_final: 0.8107 (tp30) REVERT: C 103 GLN cc_start: 0.7999 (tt0) cc_final: 0.7654 (tm-30) REVERT: C 168 LYS cc_start: 0.8512 (ttmm) cc_final: 0.8011 (mmtm) REVERT: C 217 TYR cc_start: 0.8372 (m-80) cc_final: 0.8091 (m-80) REVERT: C 355 ASN cc_start: 0.6845 (m-40) cc_final: 0.5938 (p0) REVERT: C 634 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7563 (mm-30) outliers start: 59 outliers final: 39 residues processed: 543 average time/residue: 0.1602 time to fit residues: 131.7936 Evaluate side-chains 503 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 461 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 280 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 145 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 30 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN M 6 GLN C 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.106110 restraints weight = 39430.568| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.07 r_work: 0.3194 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 24271 Z= 0.180 Angle : 0.658 12.620 33114 Z= 0.328 Chirality : 0.047 0.438 3851 Planarity : 0.004 0.041 4064 Dihedral : 8.301 67.590 4684 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 2.71 % Allowed : 13.35 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.28 (0.15), residues: 2814 helix: 1.13 (0.27), residues: 362 sheet: 0.56 (0.15), residues: 1016 loop : -0.27 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 82A TYR 0.029 0.002 TYR K 49 PHE 0.021 0.002 PHE C 53 TRP 0.022 0.002 TRP D 50 HIS 0.006 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00414 (24149) covalent geometry : angle 0.62922 (32793) SS BOND : bond 0.00598 ( 45) SS BOND : angle 1.20448 ( 90) hydrogen bonds : bond 0.04036 ( 616) hydrogen bonds : angle 5.68495 ( 1596) link_ALPHA1-2 : bond 0.00077 ( 2) link_ALPHA1-2 : angle 1.92041 ( 6) link_ALPHA1-3 : bond 0.00702 ( 6) link_ALPHA1-3 : angle 1.86544 ( 18) link_ALPHA1-6 : bond 0.01008 ( 3) link_ALPHA1-6 : angle 2.16066 ( 9) link_BETA1-4 : bond 0.00742 ( 18) link_BETA1-4 : angle 2.52284 ( 54) link_BETA1-6 : bond 0.00344 ( 2) link_BETA1-6 : angle 2.00984 ( 6) link_NAG-ASN : bond 0.00346 ( 46) link_NAG-ASN : angle 2.31954 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 484 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.8089 (t0) cc_final: 0.7834 (t0) REVERT: A 616 ASN cc_start: 0.8860 (p0) cc_final: 0.8461 (p0) REVERT: A 632 GLU cc_start: 0.8783 (tp30) cc_final: 0.8497 (tp30) REVERT: D 58 ASN cc_start: 0.8063 (t0) cc_final: 0.7657 (t0) REVERT: D 79 TYR cc_start: 0.8360 (m-80) cc_final: 0.8126 (m-10) REVERT: D 80 MET cc_start: 0.8330 (tmm) cc_final: 0.7823 (tmm) REVERT: H 13 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7817 (mtp-110) REVERT: H 81 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8746 (mmmm) REVERT: E 58 ILE cc_start: 0.6856 (mm) cc_final: 0.6469 (mt) REVERT: F 3 GLN cc_start: 0.8566 (tp-100) cc_final: 0.8183 (tp-100) REVERT: F 19 LYS cc_start: 0.7476 (ttmt) cc_final: 0.7041 (ttmm) REVERT: F 32 TYR cc_start: 0.8574 (m-80) cc_final: 0.8365 (m-10) REVERT: F 57 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8386 (mttt) REVERT: F 66 ARG cc_start: 0.6737 (ttm170) cc_final: 0.6529 (ttt180) REVERT: F 82 ARG cc_start: 0.7141 (mtp180) cc_final: 0.6862 (mtm-85) REVERT: L 4 MET cc_start: 0.8802 (mmm) cc_final: 0.8386 (mmm) REVERT: G 12 SER cc_start: 0.8775 (t) cc_final: 0.8509 (m) REVERT: G 54 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.7874 (mtp180) REVERT: G 86 TYR cc_start: 0.8241 (m-10) cc_final: 0.7901 (m-10) REVERT: G 91 TYR cc_start: 0.8870 (p90) cc_final: 0.8598 (p90) REVERT: J 46 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7513 (tm-30) REVERT: J 57 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8513 (mtpt) REVERT: J 58 ASN cc_start: 0.8202 (m-40) cc_final: 0.7828 (m-40) REVERT: J 90 TYR cc_start: 0.7715 (m-80) cc_final: 0.7284 (m-80) REVERT: K 17 GLN cc_start: 0.7564 (tt0) cc_final: 0.7289 (pt0) REVERT: K 29 SER cc_start: 0.8565 (t) cc_final: 0.8253 (p) REVERT: K 86 TYR cc_start: 0.8988 (m-80) cc_final: 0.8756 (m-80) REVERT: B 35 TRP cc_start: 0.8406 (m100) cc_final: 0.8054 (m100) REVERT: B 110 SER cc_start: 0.9157 (t) cc_final: 0.8557 (m) REVERT: B 126 CYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7351 (t) REVERT: B 160 ASN cc_start: 0.8318 (m-40) cc_final: 0.7714 (p0) REVERT: B 189 THR cc_start: 0.9149 (p) cc_final: 0.8468 (t) REVERT: B 217 TYR cc_start: 0.9149 (m-80) cc_final: 0.8278 (m-80) REVERT: B 446 SER cc_start: 0.9146 (t) cc_final: 0.8617 (p) REVERT: B 490 LYS cc_start: 0.8921 (tttm) cc_final: 0.8577 (tttp) REVERT: B 500 ARG cc_start: 0.6877 (mtm180) cc_final: 0.6556 (ptt90) REVERT: I 81 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8340 (ttpp) REVERT: M 42 LYS cc_start: 0.7993 (mmmm) cc_final: 0.7696 (mmmt) REVERT: M 79 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8446 (mm110) REVERT: C 103 GLN cc_start: 0.8059 (tt0) cc_final: 0.7624 (tm-30) REVERT: C 168 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8015 (mmtt) REVERT: C 217 TYR cc_start: 0.8562 (m-80) cc_final: 0.8185 (m-80) REVERT: C 355 ASN cc_start: 0.7040 (m-40) cc_final: 0.6043 (p0) REVERT: C 634 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7499 (mm-30) outliers start: 68 outliers final: 51 residues processed: 519 average time/residue: 0.1676 time to fit residues: 131.6570 Evaluate side-chains 501 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 449 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain G residue 83 GLU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 445 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 103 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 224 optimal weight: 0.2980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 249 HIS A 575 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN G 6 GLN ** J 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096620 restraints weight = 39341.419| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 3.05 r_work: 0.3101 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24271 Z= 0.277 Angle : 0.718 14.666 33114 Z= 0.358 Chirality : 0.049 0.395 3851 Planarity : 0.005 0.054 4064 Dihedral : 7.544 59.357 4684 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.58 % Favored : 95.24 % Rotamer: Outliers : 3.39 % Allowed : 13.75 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.10 (0.15), residues: 2814 helix: 0.98 (0.27), residues: 360 sheet: 0.24 (0.15), residues: 998 loop : -0.49 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 38 TYR 0.046 0.002 TYR M 49 PHE 0.022 0.002 PHE C 53 TRP 0.020 0.002 TRP D 50 HIS 0.007 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00649 (24149) covalent geometry : angle 0.69040 (32793) SS BOND : bond 0.00725 ( 45) SS BOND : angle 1.35709 ( 90) hydrogen bonds : bond 0.04226 ( 616) hydrogen bonds : angle 5.65267 ( 1596) link_ALPHA1-2 : bond 0.00198 ( 2) link_ALPHA1-2 : angle 2.00520 ( 6) link_ALPHA1-3 : bond 0.00707 ( 6) link_ALPHA1-3 : angle 1.96160 ( 18) link_ALPHA1-6 : bond 0.01101 ( 3) link_ALPHA1-6 : angle 2.20152 ( 9) link_BETA1-4 : bond 0.00695 ( 18) link_BETA1-4 : angle 2.53446 ( 54) link_BETA1-6 : bond 0.00105 ( 2) link_BETA1-6 : angle 2.19387 ( 6) link_NAG-ASN : bond 0.00434 ( 46) link_NAG-ASN : angle 2.35832 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 468 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: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7182 (t80) REVERT: A 632 GLU cc_start: 0.8855 (tp30) cc_final: 0.8565 (tp30) REVERT: D 58 ASN cc_start: 0.8048 (t0) cc_final: 0.7618 (t0) REVERT: D 66 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7338 (ttp-170) REVERT: D 79 TYR cc_start: 0.8436 (m-80) cc_final: 0.8194 (m-10) REVERT: D 80 MET cc_start: 0.8352 (tmm) cc_final: 0.7859 (tmm) REVERT: H 13 ARG cc_start: 0.8238 (mtt-85) cc_final: 0.7815 (mtp-110) REVERT: F 3 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8390 (tp-100) REVERT: F 19 LYS cc_start: 0.7460 (ttmt) cc_final: 0.6983 (ttmm) REVERT: F 46 GLU cc_start: 0.7226 (tp30) cc_final: 0.6979 (tp30) REVERT: F 57 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8420 (mttp) REVERT: F 80 MET cc_start: 0.8212 (ppp) cc_final: 0.7773 (ptt) REVERT: F 90 TYR cc_start: 0.8872 (m-10) cc_final: 0.8615 (m-80) REVERT: L 4 MET cc_start: 0.8820 (mmm) cc_final: 0.8514 (mmm) REVERT: L 6 GLN cc_start: 0.8919 (tt0) cc_final: 0.8529 (tt0) REVERT: L 94 TYR cc_start: 0.8468 (t80) cc_final: 0.8232 (t80) REVERT: G 12 SER cc_start: 0.8683 (t) cc_final: 0.8470 (m) REVERT: G 54 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8287 (mtp180) REVERT: G 86 TYR cc_start: 0.8293 (m-10) cc_final: 0.7953 (m-10) REVERT: J 43 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7580 (mtm110) REVERT: J 57 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8505 (mtpt) REVERT: J 58 ASN cc_start: 0.7950 (m-40) cc_final: 0.7551 (m-40) REVERT: J 66 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6940 (ttp-170) REVERT: J 82 ARG cc_start: 0.7940 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: J 90 TYR cc_start: 0.7789 (m-80) cc_final: 0.7422 (m-80) REVERT: K 29 SER cc_start: 0.8591 (t) cc_final: 0.8300 (p) REVERT: B 35 TRP cc_start: 0.8459 (m100) cc_final: 0.8197 (m100) REVERT: B 126 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7600 (t) REVERT: B 217 TYR cc_start: 0.9189 (m-80) cc_final: 0.8366 (m-80) REVERT: B 232 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 277 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8522 (t80) REVERT: B 446 SER cc_start: 0.9245 (t) cc_final: 0.8730 (p) REVERT: B 490 LYS cc_start: 0.8878 (tttm) cc_final: 0.8573 (tttp) REVERT: B 500 ARG cc_start: 0.7083 (mtm180) cc_final: 0.6757 (ptt90) REVERT: I 81 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8325 (ttpp) REVERT: M 79 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8221 (mm110) REVERT: M 105 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7930 (mt-10) REVERT: C 42 VAL cc_start: 0.9367 (t) cc_final: 0.9044 (m) REVERT: C 91 GLU cc_start: 0.8321 (tp30) cc_final: 0.8009 (tp30) REVERT: C 103 GLN cc_start: 0.8063 (tt0) cc_final: 0.7650 (tm-30) REVERT: C 168 LYS cc_start: 0.8496 (ttmm) cc_final: 0.7989 (mptt) REVERT: C 217 TYR cc_start: 0.8928 (m-80) cc_final: 0.8392 (m-80) REVERT: C 573 ILE cc_start: 0.6729 (mm) cc_final: 0.6198 (mt) REVERT: C 634 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7608 (mm-30) outliers start: 85 outliers final: 65 residues processed: 515 average time/residue: 0.1642 time to fit residues: 129.5395 Evaluate side-chains 500 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 431 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 58 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 320 MET Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 626 MET Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 103 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 159 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.103081 restraints weight = 39142.511| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.07 r_work: 0.3155 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24271 Z= 0.140 Angle : 0.626 14.030 33114 Z= 0.309 Chirality : 0.046 0.411 3851 Planarity : 0.004 0.053 4064 Dihedral : 6.971 59.259 4684 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.44 % Favored : 95.34 % Rotamer: Outliers : 2.67 % Allowed : 14.94 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.02 (0.15), residues: 2814 helix: 1.22 (0.28), residues: 357 sheet: 0.31 (0.16), residues: 989 loop : -0.49 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 82A TYR 0.026 0.001 TYR M 49 PHE 0.016 0.001 PHE C 53 TRP 0.024 0.001 TRP D 50 HIS 0.007 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00317 (24149) covalent geometry : angle 0.59923 (32793) SS BOND : bond 0.00375 ( 45) SS BOND : angle 1.15368 ( 90) hydrogen bonds : bond 0.03730 ( 616) hydrogen bonds : angle 5.52642 ( 1596) link_ALPHA1-2 : bond 0.00057 ( 2) link_ALPHA1-2 : angle 1.92650 ( 6) link_ALPHA1-3 : bond 0.00965 ( 6) link_ALPHA1-3 : angle 1.72366 ( 18) link_ALPHA1-6 : bond 0.01225 ( 3) link_ALPHA1-6 : angle 2.24578 ( 9) link_BETA1-4 : bond 0.00746 ( 18) link_BETA1-4 : angle 2.24186 ( 54) link_BETA1-6 : bond 0.00368 ( 2) link_BETA1-6 : angle 2.00877 ( 6) link_NAG-ASN : bond 0.00324 ( 46) link_NAG-ASN : angle 2.17322 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 477 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7190 (t80) REVERT: A 616 ASN cc_start: 0.9039 (p0) cc_final: 0.8679 (p0) REVERT: A 632 GLU cc_start: 0.8834 (tp30) cc_final: 0.8589 (tp30) REVERT: D 58 ASN cc_start: 0.8055 (t0) cc_final: 0.7715 (t0) REVERT: D 66 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7418 (ttp-170) REVERT: D 80 MET cc_start: 0.8405 (tmm) cc_final: 0.7854 (tmm) REVERT: D 82 ASN cc_start: 0.7862 (m110) cc_final: 0.7610 (m110) REVERT: H 13 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7681 (mtp-110) REVERT: F 3 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8357 (tp-100) REVERT: F 19 LYS cc_start: 0.7380 (ttmt) cc_final: 0.6923 (ttmm) REVERT: F 32 TYR cc_start: 0.8467 (m-10) cc_final: 0.8105 (m-10) REVERT: F 46 GLU cc_start: 0.7164 (tp30) cc_final: 0.6833 (tp30) REVERT: F 57 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8361 (ttmt) REVERT: F 80 MET cc_start: 0.8177 (ppp) cc_final: 0.7559 (ptt) REVERT: F 90 TYR cc_start: 0.8839 (m-10) cc_final: 0.8533 (m-80) REVERT: L 2 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7751 (mt) REVERT: L 94 TYR cc_start: 0.8362 (t80) cc_final: 0.8145 (t80) REVERT: G 54 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8207 (mtp180) REVERT: G 86 TYR cc_start: 0.8381 (m-10) cc_final: 0.8012 (m-10) REVERT: J 57 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8543 (mtpt) REVERT: J 58 ASN cc_start: 0.7676 (m-40) cc_final: 0.7361 (m-40) REVERT: K 29 SER cc_start: 0.8567 (t) cc_final: 0.8276 (p) REVERT: K 53 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6951 (mp0) REVERT: K 79 ARG cc_start: 0.7068 (mtt-85) cc_final: 0.6701 (ptp-170) REVERT: B 35 TRP cc_start: 0.8409 (m100) cc_final: 0.8135 (m100) REVERT: B 151 ARG cc_start: 0.7670 (tpt170) cc_final: 0.7321 (tpm170) REVERT: B 217 TYR cc_start: 0.9161 (m-80) cc_final: 0.8336 (m-80) REVERT: B 232 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8407 (t) REVERT: B 277 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8563 (t80) REVERT: B 352 GLN cc_start: 0.8432 (tt0) cc_final: 0.7839 (mt0) REVERT: B 446 SER cc_start: 0.9185 (t) cc_final: 0.8661 (p) REVERT: B 490 LYS cc_start: 0.8830 (tttm) cc_final: 0.8563 (tttp) REVERT: B 500 ARG cc_start: 0.7056 (mtm180) cc_final: 0.6727 (ptt90) REVERT: I 54 ASP cc_start: 0.8795 (p0) cc_final: 0.8545 (p0) REVERT: I 81 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8265 (ttpp) REVERT: M 22 THR cc_start: 0.9443 (m) cc_final: 0.9186 (t) REVERT: M 42 LYS cc_start: 0.8241 (mmmm) cc_final: 0.7890 (mmmt) REVERT: M 79 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8586 (mm-40) REVERT: M 105 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7916 (mt-10) REVERT: C 42 VAL cc_start: 0.9317 (t) cc_final: 0.9099 (m) REVERT: C 99 ASN cc_start: 0.8456 (t0) cc_final: 0.8233 (t0) REVERT: C 103 GLN cc_start: 0.8083 (tt0) cc_final: 0.7609 (tm-30) REVERT: C 168 LYS cc_start: 0.8436 (ttmm) cc_final: 0.7965 (mmtt) REVERT: C 355 ASN cc_start: 0.6995 (m-40) cc_final: 0.6040 (p0) REVERT: C 573 ILE cc_start: 0.6661 (mm) cc_final: 0.6123 (mt) REVERT: C 634 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7682 (mm-30) outliers start: 67 outliers final: 46 residues processed: 518 average time/residue: 0.1770 time to fit residues: 138.8092 Evaluate side-chains 496 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 446 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 640 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 243 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82BASN L 34 ASN J 105 GLN K 17 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.128614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101145 restraints weight = 38987.360| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.02 r_work: 0.3166 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24271 Z= 0.138 Angle : 0.614 14.531 33114 Z= 0.301 Chirality : 0.046 0.401 3851 Planarity : 0.004 0.050 4064 Dihedral : 6.618 59.679 4684 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 3.27 % Allowed : 15.30 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.04 (0.15), residues: 2814 helix: 1.27 (0.28), residues: 358 sheet: 0.32 (0.16), residues: 985 loop : -0.55 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 82A TYR 0.023 0.001 TYR G 49 PHE 0.017 0.001 PHE C 53 TRP 0.028 0.001 TRP D 100D HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00316 (24149) covalent geometry : angle 0.58866 (32793) SS BOND : bond 0.00323 ( 45) SS BOND : angle 1.03505 ( 90) hydrogen bonds : bond 0.03605 ( 616) hydrogen bonds : angle 5.40839 ( 1596) link_ALPHA1-2 : bond 0.00070 ( 2) link_ALPHA1-2 : angle 1.93704 ( 6) link_ALPHA1-3 : bond 0.00949 ( 6) link_ALPHA1-3 : angle 1.64919 ( 18) link_ALPHA1-6 : bond 0.01251 ( 3) link_ALPHA1-6 : angle 2.19613 ( 9) link_BETA1-4 : bond 0.00728 ( 18) link_BETA1-4 : angle 2.21798 ( 54) link_BETA1-6 : bond 0.00354 ( 2) link_BETA1-6 : angle 2.03441 ( 6) link_NAG-ASN : bond 0.00318 ( 46) link_NAG-ASN : angle 2.08704 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 474 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7272 (t80) REVERT: A 616 ASN cc_start: 0.9072 (p0) cc_final: 0.8710 (p0) REVERT: A 632 GLU cc_start: 0.8843 (tp30) cc_final: 0.8635 (tp30) REVERT: A 660 LEU cc_start: 0.8114 (mp) cc_final: 0.7517 (tt) REVERT: D 58 ASN cc_start: 0.8074 (t0) cc_final: 0.7712 (t0) REVERT: D 66 ARG cc_start: 0.7855 (mtp180) cc_final: 0.7569 (ttp-170) REVERT: D 80 MET cc_start: 0.8404 (tmm) cc_final: 0.7825 (tmm) REVERT: H 13 ARG cc_start: 0.8101 (mtt-85) cc_final: 0.7621 (mtp-110) REVERT: H 58 ASN cc_start: 0.8397 (t0) cc_final: 0.7953 (t0) REVERT: F 3 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8331 (tp-100) REVERT: F 19 LYS cc_start: 0.7359 (ttmt) cc_final: 0.6895 (ttmm) REVERT: F 32 TYR cc_start: 0.8508 (m-10) cc_final: 0.8009 (m-10) REVERT: F 46 GLU cc_start: 0.7200 (tp30) cc_final: 0.6871 (tp30) REVERT: F 57 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8118 (ttmt) REVERT: F 80 MET cc_start: 0.8158 (ppp) cc_final: 0.7696 (ptt) REVERT: F 90 TYR cc_start: 0.8854 (m-10) cc_final: 0.8576 (m-80) REVERT: L 2 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7726 (mt) REVERT: G 34 SER cc_start: 0.9016 (p) cc_final: 0.8696 (m) REVERT: G 54 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8086 (mtp180) REVERT: G 86 TYR cc_start: 0.8371 (m-10) cc_final: 0.7992 (m-10) REVERT: J 57 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8542 (mtpt) REVERT: J 58 ASN cc_start: 0.7609 (m-40) cc_final: 0.7319 (m-40) REVERT: J 66 ARG cc_start: 0.6991 (ttp-170) cc_final: 0.6791 (ttp-170) REVERT: J 105 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: K 29 SER cc_start: 0.8580 (t) cc_final: 0.8289 (p) REVERT: K 53 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6991 (mp0) REVERT: B 35 TRP cc_start: 0.8389 (m100) cc_final: 0.7903 (m100) REVERT: B 151 ARG cc_start: 0.7666 (tpt170) cc_final: 0.7302 (tpm170) REVERT: B 189 THR cc_start: 0.9109 (p) cc_final: 0.8411 (t) REVERT: B 217 TYR cc_start: 0.9162 (m-80) cc_final: 0.8376 (m-80) REVERT: B 232 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8387 (t) REVERT: B 277 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8527 (t80) REVERT: B 352 GLN cc_start: 0.8418 (tt0) cc_final: 0.7799 (mt0) REVERT: B 446 SER cc_start: 0.9154 (t) cc_final: 0.8634 (p) REVERT: B 475 MET cc_start: 0.9029 (mmm) cc_final: 0.8822 (tpp) REVERT: B 490 LYS cc_start: 0.8836 (tttm) cc_final: 0.8566 (tttp) REVERT: B 500 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6734 (ptt90) REVERT: B 619 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8133 (tt) REVERT: I 54 ASP cc_start: 0.8820 (p0) cc_final: 0.8536 (p0) REVERT: I 81 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8253 (ttpp) REVERT: M 22 THR cc_start: 0.9452 (m) cc_final: 0.9201 (t) REVERT: M 42 LYS cc_start: 0.8208 (mmmm) cc_final: 0.7861 (mmmt) REVERT: M 79 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8371 (mm110) REVERT: M 94 TYR cc_start: 0.8495 (t80) cc_final: 0.8241 (t80) REVERT: C 42 VAL cc_start: 0.9308 (t) cc_final: 0.8994 (m) REVERT: C 103 GLN cc_start: 0.8131 (tt0) cc_final: 0.7705 (tm-30) REVERT: C 168 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8054 (mmtt) REVERT: C 355 ASN cc_start: 0.6971 (m-40) cc_final: 0.6034 (p0) REVERT: C 573 ILE cc_start: 0.6529 (mm) cc_final: 0.5996 (mt) REVERT: C 634 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7733 (mm-30) outliers start: 82 outliers final: 54 residues processed: 526 average time/residue: 0.1655 time to fit residues: 132.5176 Evaluate side-chains 510 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 450 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 145 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 156 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN J 105 GLN K 17 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN C 543 ASN C 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.131837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104055 restraints weight = 39268.077| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.07 r_work: 0.3170 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24271 Z= 0.130 Angle : 0.608 13.772 33114 Z= 0.298 Chirality : 0.046 0.394 3851 Planarity : 0.004 0.055 4064 Dihedral : 6.400 59.728 4684 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.66 % Favored : 95.17 % Rotamer: Outliers : 2.79 % Allowed : 16.49 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.09 (0.15), residues: 2814 helix: 1.28 (0.28), residues: 361 sheet: 0.30 (0.16), residues: 991 loop : -0.62 (0.16), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 82A TYR 0.026 0.001 TYR E 87 PHE 0.017 0.001 PHE C 53 TRP 0.028 0.001 TRP D 100D HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00296 (24149) covalent geometry : angle 0.58457 (32793) SS BOND : bond 0.00307 ( 45) SS BOND : angle 0.93589 ( 90) hydrogen bonds : bond 0.03474 ( 616) hydrogen bonds : angle 5.36665 ( 1596) link_ALPHA1-2 : bond 0.00088 ( 2) link_ALPHA1-2 : angle 1.90293 ( 6) link_ALPHA1-3 : bond 0.00967 ( 6) link_ALPHA1-3 : angle 1.58759 ( 18) link_ALPHA1-6 : bond 0.01278 ( 3) link_ALPHA1-6 : angle 2.18810 ( 9) link_BETA1-4 : bond 0.00716 ( 18) link_BETA1-4 : angle 2.15350 ( 54) link_BETA1-6 : bond 0.00379 ( 2) link_BETA1-6 : angle 2.02920 ( 6) link_NAG-ASN : bond 0.00290 ( 46) link_NAG-ASN : angle 2.03202 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 475 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7181 (t80) REVERT: A 616 ASN cc_start: 0.9145 (p0) cc_final: 0.8765 (p0) REVERT: A 632 GLU cc_start: 0.8867 (tp30) cc_final: 0.8612 (tp30) REVERT: A 660 LEU cc_start: 0.8060 (mp) cc_final: 0.7446 (tt) REVERT: D 58 ASN cc_start: 0.8082 (t0) cc_final: 0.7755 (t0) REVERT: D 66 ARG cc_start: 0.7873 (mtp180) cc_final: 0.7638 (ttp-170) REVERT: D 80 MET cc_start: 0.8464 (tmm) cc_final: 0.7849 (tmm) REVERT: D 81 GLU cc_start: 0.7161 (pt0) cc_final: 0.6869 (pt0) REVERT: H 13 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7492 (mtp-110) REVERT: H 58 ASN cc_start: 0.8390 (t0) cc_final: 0.7940 (t0) REVERT: F 3 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8292 (tp-100) REVERT: F 19 LYS cc_start: 0.7390 (ttmt) cc_final: 0.6960 (ttmm) REVERT: F 32 TYR cc_start: 0.8541 (m-10) cc_final: 0.7997 (m-10) REVERT: F 46 GLU cc_start: 0.7214 (tp30) cc_final: 0.6835 (tp30) REVERT: F 48 MET cc_start: 0.8382 (mmm) cc_final: 0.8175 (mtp) REVERT: F 57 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8336 (ttmt) REVERT: F 90 TYR cc_start: 0.8813 (m-10) cc_final: 0.8607 (m-80) REVERT: L 2 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7746 (mt) REVERT: G 9 SER cc_start: 0.7726 (t) cc_final: 0.7342 (p) REVERT: G 34 SER cc_start: 0.9016 (p) cc_final: 0.8741 (m) REVERT: G 54 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8198 (mtp180) REVERT: G 86 TYR cc_start: 0.8414 (m-10) cc_final: 0.8047 (m-10) REVERT: J 57 LYS cc_start: 0.8853 (mtpt) cc_final: 0.8547 (mtpt) REVERT: J 58 ASN cc_start: 0.7645 (m-40) cc_final: 0.7377 (m-40) REVERT: J 66 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6739 (ttp-170) REVERT: J 105 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: K 29 SER cc_start: 0.8527 (t) cc_final: 0.8237 (p) REVERT: B 110 SER cc_start: 0.9168 (t) cc_final: 0.8592 (m) REVERT: B 151 ARG cc_start: 0.7673 (tpt170) cc_final: 0.7305 (tpm170) REVERT: B 189 THR cc_start: 0.9062 (p) cc_final: 0.8372 (t) REVERT: B 217 TYR cc_start: 0.9153 (m-80) cc_final: 0.8279 (m-80) REVERT: B 232 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8464 (t) REVERT: B 277 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8483 (t80) REVERT: B 327 ARG cc_start: 0.8257 (mtp85) cc_final: 0.7882 (mtp85) REVERT: B 350 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7794 (mtt90) REVERT: B 352 GLN cc_start: 0.8412 (tt0) cc_final: 0.7822 (mt0) REVERT: B 446 SER cc_start: 0.9126 (t) cc_final: 0.8624 (p) REVERT: B 490 LYS cc_start: 0.8833 (tttm) cc_final: 0.8580 (tttp) REVERT: B 500 ARG cc_start: 0.7007 (mtm180) cc_final: 0.6712 (ptt90) REVERT: B 619 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8156 (tt) REVERT: M 22 THR cc_start: 0.9456 (m) cc_final: 0.9224 (t) REVERT: M 42 LYS cc_start: 0.8184 (mmmm) cc_final: 0.7842 (mmmt) REVERT: M 79 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8448 (mm-40) REVERT: M 94 TYR cc_start: 0.8483 (t80) cc_final: 0.8209 (t80) REVERT: C 42 VAL cc_start: 0.9315 (t) cc_final: 0.8998 (m) REVERT: C 103 GLN cc_start: 0.8160 (tt0) cc_final: 0.7790 (tm-30) REVERT: C 168 LYS cc_start: 0.8518 (ttmm) cc_final: 0.8074 (mmtt) REVERT: C 355 ASN cc_start: 0.6987 (m-40) cc_final: 0.6096 (p0) REVERT: C 502 LYS cc_start: 0.8264 (tttm) cc_final: 0.7463 (pttp) REVERT: C 573 ILE cc_start: 0.6405 (mm) cc_final: 0.5881 (mt) REVERT: C 634 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7765 (mm-30) outliers start: 70 outliers final: 50 residues processed: 516 average time/residue: 0.1614 time to fit residues: 126.4158 Evaluate side-chains 509 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 452 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.100321 restraints weight = 38946.742| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.03 r_work: 0.3162 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24271 Z= 0.156 Angle : 0.622 13.239 33114 Z= 0.306 Chirality : 0.046 0.384 3851 Planarity : 0.004 0.056 4064 Dihedral : 6.339 59.740 4684 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.02 % Rotamer: Outliers : 3.03 % Allowed : 16.73 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.14 (0.16), residues: 2814 helix: 1.30 (0.28), residues: 360 sheet: 0.22 (0.16), residues: 986 loop : -0.62 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 82A TYR 0.024 0.001 TYR G 49 PHE 0.016 0.001 PHE C 53 TRP 0.032 0.001 TRP D 100D HIS 0.007 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00362 (24149) covalent geometry : angle 0.59849 (32793) SS BOND : bond 0.00340 ( 45) SS BOND : angle 0.97364 ( 90) hydrogen bonds : bond 0.03535 ( 616) hydrogen bonds : angle 5.37179 ( 1596) link_ALPHA1-2 : bond 0.00068 ( 2) link_ALPHA1-2 : angle 1.88998 ( 6) link_ALPHA1-3 : bond 0.00902 ( 6) link_ALPHA1-3 : angle 1.60297 ( 18) link_ALPHA1-6 : bond 0.01229 ( 3) link_ALPHA1-6 : angle 2.19512 ( 9) link_BETA1-4 : bond 0.00702 ( 18) link_BETA1-4 : angle 2.16799 ( 54) link_BETA1-6 : bond 0.00302 ( 2) link_BETA1-6 : angle 2.07262 ( 6) link_NAG-ASN : bond 0.00327 ( 46) link_NAG-ASN : angle 2.08175 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 462 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7273 (t80) REVERT: A 616 ASN cc_start: 0.9179 (p0) cc_final: 0.8800 (p0) REVERT: A 632 GLU cc_start: 0.8862 (tp30) cc_final: 0.8610 (tp30) REVERT: D 58 ASN cc_start: 0.8065 (t0) cc_final: 0.7761 (t0) REVERT: D 66 ARG cc_start: 0.7882 (mtp180) cc_final: 0.7651 (ttp-170) REVERT: D 80 MET cc_start: 0.8467 (tmm) cc_final: 0.7863 (tmm) REVERT: D 81 GLU cc_start: 0.7153 (pt0) cc_final: 0.6861 (pt0) REVERT: H 13 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7571 (mtp-110) REVERT: H 58 ASN cc_start: 0.8391 (t0) cc_final: 0.7942 (t0) REVERT: F 3 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8323 (tp-100) REVERT: F 19 LYS cc_start: 0.7417 (ttmt) cc_final: 0.6971 (ttmm) REVERT: F 32 TYR cc_start: 0.8564 (m-10) cc_final: 0.8031 (m-10) REVERT: F 46 GLU cc_start: 0.7221 (tp30) cc_final: 0.6847 (tp30) REVERT: F 90 TYR cc_start: 0.8823 (m-10) cc_final: 0.8600 (m-80) REVERT: L 2 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7744 (mt) REVERT: G 9 SER cc_start: 0.7694 (t) cc_final: 0.7322 (p) REVERT: G 34 SER cc_start: 0.9031 (p) cc_final: 0.8789 (m) REVERT: G 54 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7580 (mtp180) REVERT: G 86 TYR cc_start: 0.8435 (m-10) cc_final: 0.8061 (m-10) REVERT: J 57 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8663 (mtpt) REVERT: J 66 ARG cc_start: 0.7035 (ttp-170) cc_final: 0.6755 (ttp-170) REVERT: J 105 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7854 (pm20) REVERT: K 21 ILE cc_start: 0.8895 (mt) cc_final: 0.8604 (tt) REVERT: K 29 SER cc_start: 0.8544 (t) cc_final: 0.8245 (p) REVERT: B 35 TRP cc_start: 0.8091 (m100) cc_final: 0.7421 (m100) REVERT: B 110 SER cc_start: 0.9171 (t) cc_final: 0.8594 (m) REVERT: B 151 ARG cc_start: 0.7660 (tpt170) cc_final: 0.7290 (tpm170) REVERT: B 189 THR cc_start: 0.9059 (p) cc_final: 0.8371 (t) REVERT: B 217 TYR cc_start: 0.9158 (m-80) cc_final: 0.8277 (m-80) REVERT: B 232 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8459 (t) REVERT: B 277 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8506 (t80) REVERT: B 327 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7884 (mtp85) REVERT: B 350 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7815 (mtt90) REVERT: B 352 GLN cc_start: 0.8457 (tt0) cc_final: 0.7863 (mt0) REVERT: B 446 SER cc_start: 0.9162 (t) cc_final: 0.8666 (p) REVERT: B 490 LYS cc_start: 0.8867 (tttm) cc_final: 0.8590 (tttp) REVERT: B 500 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6734 (ptt90) REVERT: B 575 GLN cc_start: 0.7985 (mm-40) cc_final: 0.6704 (pp30) REVERT: B 619 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8154 (tt) REVERT: M 22 THR cc_start: 0.9460 (m) cc_final: 0.9238 (t) REVERT: M 79 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8443 (mm-40) REVERT: M 94 TYR cc_start: 0.8510 (t80) cc_final: 0.8258 (t80) REVERT: C 42 VAL cc_start: 0.9323 (t) cc_final: 0.9004 (m) REVERT: C 103 GLN cc_start: 0.8186 (tt0) cc_final: 0.7812 (tm-30) REVERT: C 168 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8044 (mmtt) REVERT: C 355 ASN cc_start: 0.6996 (m-40) cc_final: 0.6105 (p0) REVERT: C 502 LYS cc_start: 0.8311 (tttm) cc_final: 0.7463 (pttt) REVERT: C 573 ILE cc_start: 0.6433 (mm) cc_final: 0.5910 (mt) REVERT: C 634 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7818 (mm-30) outliers start: 76 outliers final: 59 residues processed: 508 average time/residue: 0.1606 time to fit residues: 123.4103 Evaluate side-chains 515 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 449 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 112 TRP Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 125 optimal weight: 4.9990 chunk 272 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 65 optimal weight: 0.0270 chunk 79 optimal weight: 0.9990 chunk 263 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 273 optimal weight: 0.9980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN K 17 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104200 restraints weight = 39387.420| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.07 r_work: 0.3174 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24271 Z= 0.128 Angle : 0.605 13.610 33114 Z= 0.297 Chirality : 0.046 0.383 3851 Planarity : 0.004 0.054 4064 Dihedral : 6.184 57.726 4684 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 2.71 % Allowed : 17.21 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.14 (0.16), residues: 2814 helix: 1.37 (0.28), residues: 360 sheet: 0.26 (0.16), residues: 982 loop : -0.67 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 82A TYR 0.024 0.001 TYR G 49 PHE 0.014 0.001 PHE C 53 TRP 0.033 0.001 TRP D 100D HIS 0.005 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (24149) covalent geometry : angle 0.58265 (32793) SS BOND : bond 0.00294 ( 45) SS BOND : angle 0.88481 ( 90) hydrogen bonds : bond 0.03412 ( 616) hydrogen bonds : angle 5.33325 ( 1596) link_ALPHA1-2 : bond 0.00103 ( 2) link_ALPHA1-2 : angle 1.85623 ( 6) link_ALPHA1-3 : bond 0.00960 ( 6) link_ALPHA1-3 : angle 1.51991 ( 18) link_ALPHA1-6 : bond 0.01258 ( 3) link_ALPHA1-6 : angle 2.20793 ( 9) link_BETA1-4 : bond 0.00731 ( 18) link_BETA1-4 : angle 2.10742 ( 54) link_BETA1-6 : bond 0.00362 ( 2) link_BETA1-6 : angle 2.06471 ( 6) link_NAG-ASN : bond 0.00324 ( 46) link_NAG-ASN : angle 2.01670 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 468 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7210 (t80) REVERT: A 616 ASN cc_start: 0.9180 (p0) cc_final: 0.8810 (p0) REVERT: A 632 GLU cc_start: 0.8855 (tp30) cc_final: 0.8592 (tp30) REVERT: A 660 LEU cc_start: 0.8012 (mp) cc_final: 0.7483 (tt) REVERT: A 661 LEU cc_start: 0.7914 (mp) cc_final: 0.7682 (mt) REVERT: D 58 ASN cc_start: 0.8020 (t0) cc_final: 0.7671 (t0) REVERT: D 80 MET cc_start: 0.8467 (tmm) cc_final: 0.7865 (tmm) REVERT: D 81 GLU cc_start: 0.7136 (pt0) cc_final: 0.6848 (pt0) REVERT: H 13 ARG cc_start: 0.8012 (mtt-85) cc_final: 0.7539 (mtp-110) REVERT: H 58 ASN cc_start: 0.8376 (t0) cc_final: 0.7951 (t0) REVERT: H 82 MET cc_start: 0.8182 (tpp) cc_final: 0.7893 (tpp) REVERT: F 3 GLN cc_start: 0.8642 (tp-100) cc_final: 0.8370 (tp-100) REVERT: F 19 LYS cc_start: 0.7381 (ttmt) cc_final: 0.6930 (ttmm) REVERT: F 32 TYR cc_start: 0.8547 (m-10) cc_final: 0.8029 (m-10) REVERT: F 46 GLU cc_start: 0.7205 (tp30) cc_final: 0.6818 (tp30) REVERT: F 64 GLN cc_start: 0.7834 (mt0) cc_final: 0.7540 (mt0) REVERT: F 90 TYR cc_start: 0.8797 (m-10) cc_final: 0.8579 (m-80) REVERT: G 9 SER cc_start: 0.7664 (t) cc_final: 0.7303 (p) REVERT: G 34 SER cc_start: 0.9008 (p) cc_final: 0.8790 (m) REVERT: G 42 ARG cc_start: 0.8043 (ttm110) cc_final: 0.7789 (mmm-85) REVERT: G 54 ARG cc_start: 0.8394 (mtm-85) cc_final: 0.7553 (mtp180) REVERT: G 86 TYR cc_start: 0.8411 (m-10) cc_final: 0.8066 (m-10) REVERT: J 105 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: K 21 ILE cc_start: 0.8879 (mt) cc_final: 0.8602 (tt) REVERT: K 29 SER cc_start: 0.8545 (t) cc_final: 0.8254 (p) REVERT: B 35 TRP cc_start: 0.8120 (m100) cc_final: 0.7679 (m100) REVERT: B 110 SER cc_start: 0.9138 (t) cc_final: 0.8548 (m) REVERT: B 151 ARG cc_start: 0.7644 (tpt170) cc_final: 0.7264 (tpm170) REVERT: B 189 THR cc_start: 0.9060 (p) cc_final: 0.8377 (t) REVERT: B 217 TYR cc_start: 0.9133 (m-80) cc_final: 0.8285 (m-80) REVERT: B 277 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8484 (t80) REVERT: B 350 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7805 (mtt90) REVERT: B 352 GLN cc_start: 0.8470 (tt0) cc_final: 0.7923 (mt0) REVERT: B 490 LYS cc_start: 0.8853 (tttm) cc_final: 0.8592 (tttp) REVERT: B 500 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6755 (ptt90) REVERT: B 575 GLN cc_start: 0.7932 (mm-40) cc_final: 0.6731 (pp30) REVERT: B 619 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8183 (tt) REVERT: I 81 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8149 (ttpp) REVERT: I 105 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.7761 (mtm-85) REVERT: M 22 THR cc_start: 0.9470 (m) cc_final: 0.9256 (t) REVERT: M 79 GLN cc_start: 0.8674 (mm-40) cc_final: 0.8183 (mm110) REVERT: M 94 TYR cc_start: 0.8484 (t80) cc_final: 0.8231 (t80) REVERT: C 42 VAL cc_start: 0.9305 (t) cc_final: 0.8988 (m) REVERT: C 103 GLN cc_start: 0.8183 (tt0) cc_final: 0.7828 (tm-30) REVERT: C 168 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8090 (mmtt) REVERT: C 355 ASN cc_start: 0.6902 (m-40) cc_final: 0.6077 (p0) REVERT: C 502 LYS cc_start: 0.8232 (tttm) cc_final: 0.7389 (pttt) REVERT: C 573 ILE cc_start: 0.6421 (mm) cc_final: 0.5895 (mt) outliers start: 68 outliers final: 54 residues processed: 509 average time/residue: 0.1546 time to fit residues: 119.7430 Evaluate side-chains 510 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 451 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 96 ASN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain M residue 102 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 209 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 102 optimal weight: 0.0980 chunk 251 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 202 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 213 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 GLN K 17 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN I 96 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103025 restraints weight = 38833.809| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.01 r_work: 0.3191 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24271 Z= 0.116 Angle : 0.598 13.326 33114 Z= 0.295 Chirality : 0.045 0.385 3851 Planarity : 0.004 0.063 4064 Dihedral : 6.090 57.081 4684 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.80 % Favored : 95.02 % Rotamer: Outliers : 2.51 % Allowed : 17.45 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.11 (0.16), residues: 2814 helix: 1.38 (0.28), residues: 362 sheet: 0.31 (0.16), residues: 978 loop : -0.67 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 82A TYR 0.024 0.001 TYR G 49 PHE 0.013 0.001 PHE C 53 TRP 0.034 0.001 TRP D 100D HIS 0.004 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00261 (24149) covalent geometry : angle 0.57575 (32793) SS BOND : bond 0.00272 ( 45) SS BOND : angle 0.85173 ( 90) hydrogen bonds : bond 0.03352 ( 616) hydrogen bonds : angle 5.29605 ( 1596) link_ALPHA1-2 : bond 0.00114 ( 2) link_ALPHA1-2 : angle 1.86416 ( 6) link_ALPHA1-3 : bond 0.00971 ( 6) link_ALPHA1-3 : angle 1.50565 ( 18) link_ALPHA1-6 : bond 0.01228 ( 3) link_ALPHA1-6 : angle 2.21704 ( 9) link_BETA1-4 : bond 0.00724 ( 18) link_BETA1-4 : angle 2.07169 ( 54) link_BETA1-6 : bond 0.00403 ( 2) link_BETA1-6 : angle 2.04992 ( 6) link_NAG-ASN : bond 0.00317 ( 46) link_NAG-ASN : angle 1.99086 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5628 Ramachandran restraints generated. 2814 Oldfield, 0 Emsley, 2814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 471 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7216 (t80) REVERT: A 616 ASN cc_start: 0.9174 (p0) cc_final: 0.8805 (p0) REVERT: A 632 GLU cc_start: 0.8854 (tp30) cc_final: 0.8590 (tp30) REVERT: A 660 LEU cc_start: 0.7998 (mp) cc_final: 0.7472 (tt) REVERT: A 661 LEU cc_start: 0.7925 (mp) cc_final: 0.7707 (mt) REVERT: D 58 ASN cc_start: 0.8071 (t0) cc_final: 0.7673 (t0) REVERT: D 66 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.7597 (ttp80) REVERT: D 80 MET cc_start: 0.8457 (tmm) cc_final: 0.7856 (tmm) REVERT: D 81 GLU cc_start: 0.7217 (pt0) cc_final: 0.6961 (pt0) REVERT: H 13 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7567 (mtp-110) REVERT: H 58 ASN cc_start: 0.8257 (t0) cc_final: 0.7835 (t0) REVERT: H 82 MET cc_start: 0.8201 (tpp) cc_final: 0.7904 (tpp) REVERT: F 3 GLN cc_start: 0.8645 (tp-100) cc_final: 0.8379 (tp-100) REVERT: F 19 LYS cc_start: 0.7416 (ttmt) cc_final: 0.6967 (ttmm) REVERT: F 32 TYR cc_start: 0.8504 (m-10) cc_final: 0.7980 (m-10) REVERT: F 46 GLU cc_start: 0.7163 (tp30) cc_final: 0.6769 (tp30) REVERT: F 64 GLN cc_start: 0.7808 (mt0) cc_final: 0.7512 (mt0) REVERT: F 68 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7636 (tt) REVERT: F 90 TYR cc_start: 0.8777 (m-10) cc_final: 0.8567 (m-80) REVERT: G 9 SER cc_start: 0.7633 (t) cc_final: 0.7289 (p) REVERT: G 34 SER cc_start: 0.8996 (p) cc_final: 0.8787 (m) REVERT: G 42 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7779 (mmm-85) REVERT: G 54 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7529 (mtp180) REVERT: G 74 THR cc_start: 0.8079 (m) cc_final: 0.7871 (m) REVERT: G 86 TYR cc_start: 0.8378 (m-10) cc_final: 0.8057 (m-10) REVERT: K 21 ILE cc_start: 0.8866 (mt) cc_final: 0.8608 (tt) REVERT: K 29 SER cc_start: 0.8537 (t) cc_final: 0.8204 (p) REVERT: B 35 TRP cc_start: 0.8145 (m100) cc_final: 0.7760 (m100) REVERT: B 110 SER cc_start: 0.9131 (t) cc_final: 0.8545 (m) REVERT: B 151 ARG cc_start: 0.7697 (tpt170) cc_final: 0.7274 (tpm170) REVERT: B 189 THR cc_start: 0.9056 (p) cc_final: 0.8378 (t) REVERT: B 217 TYR cc_start: 0.9134 (m-80) cc_final: 0.8268 (m-80) REVERT: B 277 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 350 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7808 (mtt90) REVERT: B 352 GLN cc_start: 0.8441 (tt0) cc_final: 0.7902 (mt0) REVERT: B 490 LYS cc_start: 0.8809 (tttm) cc_final: 0.8550 (tttp) REVERT: B 500 ARG cc_start: 0.7140 (mtm180) cc_final: 0.6747 (ptt90) REVERT: B 575 GLN cc_start: 0.7962 (mm-40) cc_final: 0.6762 (pp30) REVERT: B 619 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8246 (tt) REVERT: I 81 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8153 (ttpp) REVERT: I 105 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.7739 (mtm-85) REVERT: M 42 LYS cc_start: 0.8170 (mmmm) cc_final: 0.7775 (mmmt) REVERT: M 79 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8454 (mm-40) REVERT: M 94 TYR cc_start: 0.8465 (t80) cc_final: 0.8211 (t80) REVERT: C 103 GLN cc_start: 0.8166 (tt0) cc_final: 0.7814 (tm-30) REVERT: C 168 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8097 (mmtm) REVERT: C 355 ASN cc_start: 0.6881 (m-40) cc_final: 0.6075 (p0) REVERT: C 502 LYS cc_start: 0.8230 (tttm) cc_final: 0.7332 (pttt) REVERT: C 573 ILE cc_start: 0.6440 (mm) cc_final: 0.5903 (mt) outliers start: 63 outliers final: 50 residues processed: 506 average time/residue: 0.1669 time to fit residues: 127.9175 Evaluate side-chains 503 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 448 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 277 PHE Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 GLN Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 42 ARG Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 79 TYR Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 100 TRP Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 83 PHE Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain K residue 17 GLN Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 89 CYS Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 277 PHE Chi-restraints excluded: chain B residue 350 ARG Chi-restraints excluded: chain B residue 354 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 97 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 545 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 112 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 201 optimal weight: 0.2980 chunk 135 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 198 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** B 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN B 652 GLN I 96 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN C 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102679 restraints weight = 39328.474| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.05 r_work: 0.3164 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24271 Z= 0.157 Angle : 0.621 13.736 33114 Z= 0.307 Chirality : 0.046 0.383 3851 Planarity : 0.004 0.057 4064 Dihedral : 6.093 57.481 4684 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.83 % Favored : 95.02 % Rotamer: Outliers : 2.55 % Allowed : 17.61 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.13 (0.16), residues: 2814 helix: 1.31 (0.28), residues: 363 sheet: 0.27 (0.16), residues: 973 loop : -0.64 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 82A TYR 0.027 0.001 TYR G 49 PHE 0.014 0.001 PHE C 53 TRP 0.036 0.001 TRP D 100D HIS 0.005 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00366 (24149) covalent geometry : angle 0.59859 (32793) SS BOND : bond 0.00332 ( 45) SS BOND : angle 0.95808 ( 90) hydrogen bonds : bond 0.03500 ( 616) hydrogen bonds : angle 5.31419 ( 1596) link_ALPHA1-2 : bond 0.00046 ( 2) link_ALPHA1-2 : angle 1.84773 ( 6) link_ALPHA1-3 : bond 0.00859 ( 6) link_ALPHA1-3 : angle 1.56987 ( 18) link_ALPHA1-6 : bond 0.01184 ( 3) link_ALPHA1-6 : angle 2.18015 ( 9) link_BETA1-4 : bond 0.00702 ( 18) link_BETA1-4 : angle 2.09834 ( 54) link_BETA1-6 : bond 0.00274 ( 2) link_BETA1-6 : angle 2.10939 ( 6) link_NAG-ASN : bond 0.00313 ( 46) link_NAG-ASN : angle 2.02965 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4896.01 seconds wall clock time: 84 minutes 59.31 seconds (5099.31 seconds total)