Starting phenix.real_space_refine on Sun Aug 24 13:33:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sb2_40288/08_2025/8sb2_40288.map" } resolution = 3.5 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= 0.010 sd= 0.240 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 141 5.16 5 C 12585 2.51 5 N 3321 2.21 5 O 4139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20186 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "B" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "C" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "G" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "I" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 23, 'TRANS': 434} Chain: "L" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain: "M" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 987 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "N" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 798 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" 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: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "X" 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: "Y" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 127 Unusual residues: {'BMA': 1, 'MAN': 8, 'NAG': 2} 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: "Z" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" 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 Time building chain proxies: 4.16, per 1000 atoms: 0.21 Number of scatterers: 20186 At special positions: 0 Unit cell: (159.84, 156.6, 139.32, 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 141 16.00 O 4139 8.00 N 3321 7.00 C 12585 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=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " 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=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 433 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 101 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.04 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.03 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.03 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.03 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.03 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS K 501 " - pdb=" SG CYS L 605 " distance=2.03 Simple disulfide: pdb=" SG CYS L 598 " - pdb=" SG CYS L 604 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM19206 O5 NAG E 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN J 4 " - " MAN J 5 " " MAN O 4 " - " MAN O 5 " " MAN O 5 " - " MAN O 6 " " MAN O 8 " - " MAN O 9 " " MAN O 10 " - " MAN O 11 " " MAN T 4 " - " MAN T 5 " " MAN T 5 " - " MAN T 6 " " MAN T 8 " - " MAN T 9 " " MAN T 10 " - " MAN T 11 " " MAN X 4 " - " MAN X 5 " " MAN Y 4 " - " MAN Y 5 " " MAN Y 5 " - " MAN Y 6 " " MAN Y 8 " - " MAN Y 9 " " MAN Y 10 " - " MAN Y 11 " ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA O 3 " - " MAN O 4 " " MAN O 7 " - " MAN O 8 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 7 " - " MAN T 8 " " BMA X 3 " - " MAN X 4 " " BMA Y 3 " - " MAN Y 4 " " MAN Y 7 " - " MAN Y 8 " " MAN Z 4 " - " MAN Z 5 " ALPHA1-6 " BMA O 3 " - " MAN O 7 " " MAN O 7 " - " MAN O 10 " " BMA P 3 " - " MAN P 4 " " MAN P 4 " - " MAN P 6 " " BMA T 3 " - " MAN T 7 " " MAN T 7 " - " MAN T 10 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA Y 3 " - " MAN Y 7 " " MAN Y 7 " - " MAN Y 10 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 6 " " BMA a 3 " - " MAN a 4 " " MAN a 4 " - " MAN a 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " NAG-ASN " NAG E 1 " - " ASN A 138 " " NAG J 1 " - " ASN A 301 " " NAG O 1 " - " ASN A 332 " " NAG P 1 " - " ASN A 156 " " NAG Q 1 " - " ASN A 442 " " NAG R 1 " - " ASN F 138 " " NAG S 1 " - " ASN F 301 " " NAG T 1 " - " ASN F 332 " " NAG U 1 " - " ASN F 156 " " NAG V 1 " - " ASN F 442 " " NAG W 1 " - " ASN K 138 " " NAG X 1 " - " ASN K 301 " " NAG Y 1 " - " ASN K 332 " " NAG Z 1 " - " ASN K 156 " " NAG a 1 " - " ASN K 442 " Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 877.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4554 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 45 sheets defined 17.4% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 removed outlier: 3.680A pdb=" N ALA A 60 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 3.797A pdb=" N HIS A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.503A pdb=" N THR A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 481 removed outlier: 3.734A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.893A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 596 removed outlier: 3.602A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA B 578 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 588 " --> pdb=" O GLU B 584 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.631A pdb=" N SER B 615 " --> pdb=" O SER B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 636 removed outlier: 4.233A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 644 Processing helix chain 'B' and resid 649 through 663 removed outlier: 3.985A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.941A pdb=" N GLU D 85 " --> pdb=" O ALA D 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 63 removed outlier: 3.677A pdb=" N ALA F 60 " --> pdb=" O ASP F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 3.787A pdb=" N HIS F 72 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA F 73 " --> pdb=" O TRP F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.537A pdb=" N LEU F 116 " --> pdb=" O TRP F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 351 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 481 removed outlier: 3.736A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.765A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 571 through 596 removed outlier: 3.632A pdb=" N GLN G 575 " --> pdb=" O TRP G 571 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLN G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA G 578 " --> pdb=" O LYS G 574 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA G 582 " --> pdb=" O ALA G 578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL G 583 " --> pdb=" O ARG G 579 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG G 585 " --> pdb=" O LEU G 581 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 593 " --> pdb=" O ASP G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 611 through 615 removed outlier: 3.680A pdb=" N SER G 615 " --> pdb=" O SER G 612 " (cutoff:3.500A) Processing helix chain 'G' and resid 619 through 624 Processing helix chain 'G' and resid 627 through 636 removed outlier: 4.030A pdb=" N LYS G 633 " --> pdb=" O LEU G 629 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 634 " --> pdb=" O GLN G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 646 Processing helix chain 'G' and resid 650 through 654 Processing helix chain 'G' and resid 655 through 662 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.525A pdb=" N ASP I 84 " --> pdb=" O GLN I 81 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 85' Processing helix chain 'K' and resid 57 through 63 removed outlier: 3.692A pdb=" N ALA K 60 " --> pdb=" O ASP K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 74 removed outlier: 3.791A pdb=" N HIS K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA K 73 " --> pdb=" O TRP K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 115 Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 368 through 373 Processing helix chain 'K' and resid 475 through 481 removed outlier: 3.767A pdb=" N TRP K 479 " --> pdb=" O MET K 475 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER K 481 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 543 removed outlier: 3.926A pdb=" N GLN L 540 " --> pdb=" O THR L 536 " (cutoff:3.500A) Processing helix chain 'L' and resid 571 through 596 removed outlier: 3.565A pdb=" N GLN L 575 " --> pdb=" O TRP L 571 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN L 577 " --> pdb=" O ILE L 573 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA L 578 " --> pdb=" O LYS L 574 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 582 " --> pdb=" O ALA L 578 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL L 583 " --> pdb=" O ARG L 579 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG L 585 " --> pdb=" O LEU L 581 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP L 589 " --> pdb=" O ARG L 585 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU L 593 " --> pdb=" O ASP L 589 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY L 594 " --> pdb=" O GLN L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 615 removed outlier: 3.650A pdb=" N SER L 615 " --> pdb=" O SER L 612 " (cutoff:3.500A) Processing helix chain 'L' and resid 619 through 624 Processing helix chain 'L' and resid 627 through 636 removed outlier: 4.148A pdb=" N LYS L 633 " --> pdb=" O LEU L 629 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU L 634 " --> pdb=" O GLN L 630 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 646 Processing helix chain 'L' and resid 649 through 663 removed outlier: 3.659A pdb=" N GLN L 653 " --> pdb=" O SER L 649 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.550A pdb=" N ASP N 84 " --> pdb=" O GLN N 81 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU N 85 " --> pdb=" O ALA N 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.063A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 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 169 through 177 removed outlier: 6.694A pdb=" N MET A 154 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 134 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.545A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 11.127A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.626A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.841A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 308 removed outlier: 5.637A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 359 through 361 removed outlier: 3.600A pdb=" N GLY A 393 " --> pdb=" O TYR A 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.151A pdb=" N TYR C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL D 35 " --> pdb=" O TYR D 51 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TYR D 51 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.526A pdb=" N THR D 108 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 23 Processing sheet with id=AB7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.495A pdb=" N VAL F 36 " --> pdb=" O THR G 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 removed outlier: 3.514A pdb=" N LEU F 84 " --> pdb=" O THR F 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 removed outlier: 6.759A pdb=" N MET F 154 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA F 134 " --> pdb=" O MET F 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 202 through 203 removed outlier: 6.560A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.568A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER F 334 " --> pdb=" O GLU F 293 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 271 through 273 removed outlier: 11.046A pdb=" N VAL F 286 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N THR F 455 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 12.241A pdb=" N LEU F 288 " --> pdb=" O LEU F 453 " (cutoff:3.500A) removed outlier: 11.804A pdb=" N LEU F 453 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N THR F 290 " --> pdb=" O GLY F 451 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY F 451 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 302 through 308 removed outlier: 5.587A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 359 through 361 removed outlier: 3.597A pdb=" N GLY F 393 " --> pdb=" O TYR F 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.016A pdb=" N TYR H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL I 35 " --> pdb=" O TYR I 51 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR I 51 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.511A pdb=" N THR I 108 " --> pdb=" O VAL I 10 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 17 through 23 removed outlier: 3.541A pdb=" N THR I 72 " --> pdb=" O SER I 69 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 494 through 499 removed outlier: 5.242A pdb=" N VAL L 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N VAL K 38 " --> pdb=" O THR L 606 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR L 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TYR K 40 " --> pdb=" O CYS L 604 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS L 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'K' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'K' and resid 169 through 177 removed outlier: 6.682A pdb=" N MET K 154 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA K 134 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 202 through 203 removed outlier: 6.540A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.569A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLU K 293 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER K 334 " --> pdb=" O GLU K 293 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 271 through 273 removed outlier: 11.032A pdb=" N VAL K 286 " --> pdb=" O THR K 455 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N THR K 455 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N LEU K 288 " --> pdb=" O LEU K 453 " (cutoff:3.500A) removed outlier: 11.812A pdb=" N LEU K 453 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 10.328A pdb=" N THR K 290 " --> pdb=" O GLY K 451 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY K 451 " --> pdb=" O THR K 290 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 304 through 308 Processing sheet with id=AE4, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.631A pdb=" N GLY K 393 " --> pdb=" O TYR K 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'M' and resid 10 through 12 removed outlier: 5.170A pdb=" N TYR M 33 " --> pdb=" O GLY M 99 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL N 35 " --> pdb=" O TYR N 51 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR N 51 " --> pdb=" O VAL N 35 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP N 37 " --> pdb=" O MET N 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.524A pdb=" N THR N 108 " --> pdb=" O VAL N 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.537A pdb=" N THR N 72 " --> pdb=" O SER N 69 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1821 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6211 1.34 - 1.46: 5249 1.46 - 1.59: 8953 1.59 - 1.71: 1 1.71 - 1.84: 192 Bond restraints: 20606 Sorted by residual: bond pdb=" C THR A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.01e+01 bond pdb=" C THR F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.334 1.378 -0.044 8.40e-03 1.42e+04 2.76e+01 bond pdb=" C1 MAN T 11 " pdb=" C2 MAN T 11 " ideal model delta sigma weight residual 1.526 1.593 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 MAN Y 7 " pdb=" O5 MAN Y 7 " ideal model delta sigma weight residual 1.418 1.482 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C5 MAN O 7 " pdb=" O5 MAN O 7 " ideal model delta sigma weight residual 1.418 1.481 -0.063 2.00e-02 2.50e+03 9.78e+00 ... (remaining 20601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 27260 3.01 - 6.03: 653 6.03 - 9.04: 107 9.04 - 12.06: 5 12.06 - 15.07: 4 Bond angle restraints: 28029 Sorted by residual: angle pdb=" C ASN K 138 " pdb=" CA ASN K 138 " pdb=" CB ASN K 138 " ideal model delta sigma weight residual 111.82 120.72 -8.90 1.28e+00 6.10e-01 4.84e+01 angle pdb=" N ASP D 33 " pdb=" CA ASP D 33 " pdb=" C ASP D 33 " ideal model delta sigma weight residual 113.17 104.56 8.61 1.26e+00 6.30e-01 4.67e+01 angle pdb=" N ASP N 33 " pdb=" CA ASP N 33 " pdb=" C ASP N 33 " ideal model delta sigma weight residual 113.17 104.71 8.46 1.26e+00 6.30e-01 4.51e+01 angle pdb=" N SER B 649 " pdb=" CA SER B 649 " pdb=" C SER B 649 " ideal model delta sigma weight residual 110.06 119.45 -9.39 1.43e+00 4.89e-01 4.31e+01 angle pdb=" N ASP I 33 " pdb=" CA ASP I 33 " pdb=" C ASP I 33 " ideal model delta sigma weight residual 113.28 105.37 7.91 1.22e+00 6.72e-01 4.21e+01 ... (remaining 28024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.11: 12606 23.11 - 46.21: 493 46.21 - 69.31: 101 69.31 - 92.42: 97 92.42 - 115.52: 48 Dihedral angle restraints: 13345 sinusoidal: 6220 harmonic: 7125 Sorted by residual: dihedral pdb=" CB CYS K 501 " pdb=" SG CYS K 501 " pdb=" SG CYS L 605 " pdb=" CB CYS L 605 " ideal model delta sinusoidal sigma weight residual 93.00 27.72 65.28 1 1.00e+01 1.00e-02 5.59e+01 dihedral pdb=" CA GLY K 431 " pdb=" C GLY K 431 " pdb=" N ARG K 432 " pdb=" CA ARG K 432 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLY A 431 " pdb=" C GLY A 431 " pdb=" N ARG A 432 " pdb=" CA ARG A 432 " ideal model delta harmonic sigma weight residual -180.00 -146.90 -33.10 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 13342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2710 0.070 - 0.139: 554 0.139 - 0.209: 100 0.209 - 0.278: 22 0.278 - 0.348: 12 Chirality restraints: 3398 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 4.62e+00 chirality pdb=" CB VAL L 513 " pdb=" CA VAL L 513 " pdb=" CG1 VAL L 513 " pdb=" CG2 VAL L 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 3395 not shown) Planarity restraints: 3471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.001 2.00e-02 2.50e+03 6.40e-02 5.12e+01 pdb=" CG ASN A 138 " 0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.090 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN K 156 " -0.027 2.00e-02 2.50e+03 2.46e-02 7.58e+00 pdb=" CG ASN K 156 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN K 156 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN K 156 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Z 1 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 178 " 0.045 5.00e-02 4.00e+02 6.75e-02 7.28e+00 pdb=" N PRO F 179 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 3468 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4545 2.79 - 3.32: 17566 3.32 - 3.85: 32311 3.85 - 4.37: 37854 4.37 - 4.90: 66433 Nonbonded interactions: 158709 Sorted by model distance: nonbonded pdb=" O MET A 369 " pdb=" OG1 THR A 373 " model vdw 2.266 3.040 nonbonded pdb=" OD2 ASP K 325 " pdb=" OH TYR M 33 " model vdw 2.271 3.040 nonbonded pdb=" O MET K 369 " pdb=" OG1 THR K 373 " model vdw 2.273 3.040 nonbonded pdb=" O MET F 369 " pdb=" OG1 THR F 373 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR N 48 " pdb=" O3 MAN Y 5 " model vdw 2.288 3.040 ... (remaining 158704 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' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'J' selection = chain 'U' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'O' selection = chain 'T' selection = chain 'Y' } ncs_group { reference = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 20733 Z= 0.321 Angle : 1.162 30.074 28365 Z= 0.590 Chirality : 0.063 0.348 3398 Planarity : 0.007 0.087 3456 Dihedral : 16.754 115.525 8656 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.38 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.16), residues: 2454 helix: -2.95 (0.20), residues: 375 sheet: -0.06 (0.19), residues: 744 loop : -1.71 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG L 585 TYR 0.024 0.002 TYR M 27 PHE 0.012 0.002 PHE K 376 TRP 0.035 0.003 TRP A 45 HIS 0.010 0.001 HIS M 116 Details of bonding type rmsd covalent geometry : bond 0.00639 (20606) covalent geometry : angle 1.10040 (28029) SS BOND : bond 0.00304 ( 45) SS BOND : angle 1.53652 ( 90) hydrogen bonds : bond 0.15952 ( 653) hydrogen bonds : angle 8.12926 ( 1821) link_ALPHA1-2 : bond 0.00975 ( 14) link_ALPHA1-2 : angle 2.72986 ( 42) link_ALPHA1-3 : bond 0.00931 ( 12) link_ALPHA1-3 : angle 1.85466 ( 36) link_ALPHA1-6 : bond 0.00698 ( 14) link_ALPHA1-6 : angle 2.25093 ( 42) link_BETA1-4 : bond 0.01466 ( 27) link_BETA1-4 : angle 3.91328 ( 81) link_NAG-ASN : bond 0.00938 ( 15) link_NAG-ASN : angle 7.03694 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8965 (mtp) cc_final: 0.8618 (mtp) REVERT: A 426 MET cc_start: 0.7231 (ptt) cc_final: 0.6371 (tpt) REVERT: C 25 SER cc_start: 0.7710 (p) cc_final: 0.6852 (p) REVERT: F 34 LEU cc_start: 0.6165 (mt) cc_final: 0.5912 (pt) REVERT: L 584 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7579 (mm-30) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1395 time to fit residues: 52.2075 Evaluate side-chains 178 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS C 13 ASN D 16 GLN F 105 HIS F 374 HIS G 543 ASN K 105 HIS K 374 HIS N 16 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.167942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.162435 restraints weight = 28867.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.152205 restraints weight = 52313.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149481 restraints weight = 48968.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.149331 restraints weight = 45924.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.149377 restraints weight = 41487.222| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20733 Z= 0.219 Angle : 0.802 11.744 28365 Z= 0.395 Chirality : 0.051 0.263 3398 Planarity : 0.005 0.058 3456 Dihedral : 13.094 97.757 4276 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.72 % Rotamer: Outliers : 1.60 % Allowed : 6.76 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.16), residues: 2454 helix: -2.45 (0.22), residues: 372 sheet: -0.09 (0.19), residues: 723 loop : -1.47 (0.16), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 57 TYR 0.026 0.002 TYR I 51 PHE 0.016 0.002 PHE N 93 TRP 0.020 0.002 TRP H 50 HIS 0.006 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00519 (20606) covalent geometry : angle 0.75935 (28029) SS BOND : bond 0.00348 ( 45) SS BOND : angle 0.83589 ( 90) hydrogen bonds : bond 0.04934 ( 653) hydrogen bonds : angle 6.43139 ( 1821) link_ALPHA1-2 : bond 0.01017 ( 14) link_ALPHA1-2 : angle 2.26206 ( 42) link_ALPHA1-3 : bond 0.01017 ( 12) link_ALPHA1-3 : angle 1.91747 ( 36) link_ALPHA1-6 : bond 0.00616 ( 14) link_ALPHA1-6 : angle 2.02659 ( 42) link_BETA1-4 : bond 0.00838 ( 27) link_BETA1-4 : angle 2.85468 ( 81) link_NAG-ASN : bond 0.00492 ( 15) link_NAG-ASN : angle 4.34925 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9027 (mtp) cc_final: 0.8729 (mtp) REVERT: I 33 ASP cc_start: 0.7808 (t0) cc_final: 0.7509 (t0) REVERT: L 584 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7588 (mm-30) outliers start: 34 outliers final: 27 residues processed: 211 average time/residue: 0.1351 time to fit residues: 44.7001 Evaluate side-chains 194 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 99 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 168 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 135 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 183 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 218 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 577 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.169171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.163718 restraints weight = 29034.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154074 restraints weight = 56241.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151334 restraints weight = 52323.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.151298 restraints weight = 45553.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151245 restraints weight = 41892.100| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20733 Z= 0.156 Angle : 0.716 10.530 28365 Z= 0.349 Chirality : 0.048 0.229 3398 Planarity : 0.004 0.049 3456 Dihedral : 10.670 90.970 4276 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.81 % Favored : 95.03 % Rotamer: Outliers : 2.07 % Allowed : 10.05 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.16), residues: 2454 helix: -1.96 (0.24), residues: 372 sheet: -0.00 (0.19), residues: 720 loop : -1.31 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 63 TYR 0.024 0.002 TYR I 51 PHE 0.010 0.002 PHE D 93 TRP 0.014 0.001 TRP H 50 HIS 0.005 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00355 (20606) covalent geometry : angle 0.67905 (28029) SS BOND : bond 0.00217 ( 45) SS BOND : angle 0.72842 ( 90) hydrogen bonds : bond 0.04180 ( 653) hydrogen bonds : angle 5.87851 ( 1821) link_ALPHA1-2 : bond 0.01024 ( 14) link_ALPHA1-2 : angle 2.02859 ( 42) link_ALPHA1-3 : bond 0.01277 ( 12) link_ALPHA1-3 : angle 1.60326 ( 36) link_ALPHA1-6 : bond 0.00688 ( 14) link_ALPHA1-6 : angle 1.91754 ( 42) link_BETA1-4 : bond 0.00786 ( 27) link_BETA1-4 : angle 2.53686 ( 81) link_NAG-ASN : bond 0.00265 ( 15) link_NAG-ASN : angle 3.69697 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9008 (mtp) cc_final: 0.8479 (mtp) REVERT: A 426 MET cc_start: 0.7226 (tpt) cc_final: 0.7019 (tpp) REVERT: A 434 MET cc_start: 0.8874 (ttp) cc_final: 0.8659 (ttp) REVERT: H 25 SER cc_start: 0.7663 (p) cc_final: 0.6988 (p) REVERT: I 25 THR cc_start: 0.8845 (t) cc_final: 0.8574 (m) REVERT: I 33 ASP cc_start: 0.7736 (t0) cc_final: 0.7476 (t0) outliers start: 44 outliers final: 32 residues processed: 221 average time/residue: 0.1199 time to fit residues: 42.5818 Evaluate side-chains 205 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 103 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 202 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 116 optimal weight: 0.0670 chunk 157 optimal weight: 20.0000 chunk 196 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 126 optimal weight: 20.0000 overall best weight: 1.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.168623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.163148 restraints weight = 28930.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.153388 restraints weight = 54172.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150418 restraints weight = 50968.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150287 restraints weight = 53933.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150222 restraints weight = 44081.918| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20733 Z= 0.150 Angle : 0.693 9.632 28365 Z= 0.337 Chirality : 0.047 0.193 3398 Planarity : 0.004 0.045 3456 Dihedral : 9.680 87.443 4276 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.66 % Favored : 94.17 % Rotamer: Outliers : 2.68 % Allowed : 11.50 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.17), residues: 2454 helix: -1.73 (0.24), residues: 381 sheet: -0.01 (0.19), residues: 720 loop : -1.25 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 542 TYR 0.022 0.001 TYR I 51 PHE 0.011 0.002 PHE F 317 TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00347 (20606) covalent geometry : angle 0.65858 (28029) SS BOND : bond 0.00213 ( 45) SS BOND : angle 0.60719 ( 90) hydrogen bonds : bond 0.03907 ( 653) hydrogen bonds : angle 5.65564 ( 1821) link_ALPHA1-2 : bond 0.00930 ( 14) link_ALPHA1-2 : angle 1.96456 ( 42) link_ALPHA1-3 : bond 0.01068 ( 12) link_ALPHA1-3 : angle 1.80192 ( 36) link_ALPHA1-6 : bond 0.00571 ( 14) link_ALPHA1-6 : angle 1.88400 ( 42) link_BETA1-4 : bond 0.00669 ( 27) link_BETA1-4 : angle 2.32943 ( 81) link_NAG-ASN : bond 0.00303 ( 15) link_NAG-ASN : angle 3.58816 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9041 (mtp) cc_final: 0.8502 (mtp) REVERT: G 530 MET cc_start: 0.8132 (mmm) cc_final: 0.7277 (mtt) REVERT: I 25 THR cc_start: 0.8799 (t) cc_final: 0.8480 (m) outliers start: 57 outliers final: 44 residues processed: 216 average time/residue: 0.1219 time to fit residues: 42.6662 Evaluate side-chains 216 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 172 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 91 optimal weight: 0.3980 chunk 3 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 187 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 HIS F 287 HIS K 287 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.163489 restraints weight = 28784.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.158528 restraints weight = 52974.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154922 restraints weight = 65150.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154143 restraints weight = 67387.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153417 restraints weight = 56918.148| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20733 Z= 0.145 Angle : 0.683 9.637 28365 Z= 0.332 Chirality : 0.047 0.183 3398 Planarity : 0.004 0.043 3456 Dihedral : 9.227 85.380 4276 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 3.62 % Allowed : 11.88 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.17), residues: 2454 helix: -1.57 (0.24), residues: 381 sheet: -0.00 (0.19), residues: 720 loop : -1.23 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 585 TYR 0.019 0.001 TYR I 51 PHE 0.011 0.002 PHE F 317 TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00333 (20606) covalent geometry : angle 0.64853 (28029) SS BOND : bond 0.00209 ( 45) SS BOND : angle 0.58611 ( 90) hydrogen bonds : bond 0.03828 ( 653) hydrogen bonds : angle 5.54985 ( 1821) link_ALPHA1-2 : bond 0.00926 ( 14) link_ALPHA1-2 : angle 1.92887 ( 42) link_ALPHA1-3 : bond 0.01081 ( 12) link_ALPHA1-3 : angle 1.74949 ( 36) link_ALPHA1-6 : bond 0.00543 ( 14) link_ALPHA1-6 : angle 1.84646 ( 42) link_BETA1-4 : bond 0.00691 ( 27) link_BETA1-4 : angle 2.28276 ( 81) link_NAG-ASN : bond 0.00344 ( 15) link_NAG-ASN : angle 3.56556 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 177 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 348 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: G 530 MET cc_start: 0.8107 (mmm) cc_final: 0.7302 (mtt) REVERT: I 25 THR cc_start: 0.8749 (t) cc_final: 0.8490 (m) REVERT: M 3 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7542 (pt0) outliers start: 77 outliers final: 59 residues processed: 233 average time/residue: 0.1305 time to fit residues: 49.1954 Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 173 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 52 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 194 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.164213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.158351 restraints weight = 28703.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146170 restraints weight = 65028.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.142919 restraints weight = 69957.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142801 restraints weight = 76732.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.142730 restraints weight = 60560.038| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20733 Z= 0.252 Angle : 0.805 10.576 28365 Z= 0.392 Chirality : 0.051 0.224 3398 Planarity : 0.005 0.049 3456 Dihedral : 9.688 92.210 4276 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.11 % Rotamer: Outliers : 3.76 % Allowed : 12.91 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.16), residues: 2454 helix: -1.83 (0.24), residues: 396 sheet: -0.14 (0.18), residues: 762 loop : -1.42 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 57 TYR 0.024 0.002 TYR I 51 PHE 0.015 0.003 PHE K 376 TRP 0.019 0.002 TRP H 50 HIS 0.007 0.002 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00613 (20606) covalent geometry : angle 0.76975 (28029) SS BOND : bond 0.00296 ( 45) SS BOND : angle 0.73148 ( 90) hydrogen bonds : bond 0.04528 ( 653) hydrogen bonds : angle 5.91992 ( 1821) link_ALPHA1-2 : bond 0.00865 ( 14) link_ALPHA1-2 : angle 2.00303 ( 42) link_ALPHA1-3 : bond 0.01028 ( 12) link_ALPHA1-3 : angle 1.91622 ( 36) link_ALPHA1-6 : bond 0.00484 ( 14) link_ALPHA1-6 : angle 1.92972 ( 42) link_BETA1-4 : bond 0.00716 ( 27) link_BETA1-4 : angle 2.57644 ( 81) link_NAG-ASN : bond 0.00721 ( 15) link_NAG-ASN : angle 4.07202 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 181 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 534 SER cc_start: 0.7694 (t) cc_final: 0.7286 (m) REVERT: H 50 TRP cc_start: 0.8221 (OUTLIER) cc_final: 0.6264 (p90) REVERT: H 85 SER cc_start: 0.7432 (t) cc_final: 0.7219 (p) REVERT: I 25 THR cc_start: 0.8660 (t) cc_final: 0.8448 (m) REVERT: M 3 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: M 50 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.6768 (p90) outliers start: 80 outliers final: 57 residues processed: 240 average time/residue: 0.1325 time to fit residues: 51.4441 Evaluate side-chains 236 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 50 TRP Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 150 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 174 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.167136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.161638 restraints weight = 28762.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151269 restraints weight = 53237.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.147781 restraints weight = 56441.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147354 restraints weight = 73588.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147560 restraints weight = 57595.538| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20733 Z= 0.149 Angle : 0.719 20.371 28365 Z= 0.347 Chirality : 0.050 0.841 3398 Planarity : 0.004 0.044 3456 Dihedral : 9.292 86.201 4276 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.93 % Favored : 94.91 % Rotamer: Outliers : 3.05 % Allowed : 14.08 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.17), residues: 2454 helix: -1.47 (0.25), residues: 378 sheet: -0.07 (0.18), residues: 768 loop : -1.24 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.021 0.001 TYR G 643 PHE 0.011 0.002 PHE F 391 TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00339 (20606) covalent geometry : angle 0.67000 (28029) SS BOND : bond 0.00223 ( 45) SS BOND : angle 0.63343 ( 90) hydrogen bonds : bond 0.03957 ( 653) hydrogen bonds : angle 5.59062 ( 1821) link_ALPHA1-2 : bond 0.00873 ( 14) link_ALPHA1-2 : angle 1.90464 ( 42) link_ALPHA1-3 : bond 0.01087 ( 12) link_ALPHA1-3 : angle 1.77464 ( 36) link_ALPHA1-6 : bond 0.00500 ( 14) link_ALPHA1-6 : angle 1.84493 ( 42) link_BETA1-4 : bond 0.00663 ( 27) link_BETA1-4 : angle 2.22083 ( 81) link_NAG-ASN : bond 0.00943 ( 15) link_NAG-ASN : angle 5.20017 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 179 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8998 (mtp) cc_final: 0.8688 (mtp) REVERT: A 426 MET cc_start: 0.7226 (tpp) cc_final: 0.6555 (tpp) REVERT: B 534 SER cc_start: 0.7579 (t) cc_final: 0.7206 (m) REVERT: F 348 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6825 (mp0) REVERT: G 530 MET cc_start: 0.8053 (mmm) cc_final: 0.7352 (mtt) REVERT: H 50 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.6324 (p90) REVERT: L 518 VAL cc_start: 0.2039 (OUTLIER) cc_final: 0.1723 (p) REVERT: L 660 LEU cc_start: 0.8334 (tp) cc_final: 0.8112 (tt) REVERT: M 3 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7816 (pt0) outliers start: 65 outliers final: 54 residues processed: 229 average time/residue: 0.1352 time to fit residues: 49.7388 Evaluate side-chains 234 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 176 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 518 VAL Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 176 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 211 optimal weight: 0.0870 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 59 optimal weight: 0.0050 chunk 185 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.161286 restraints weight = 28752.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.149315 restraints weight = 60095.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.145905 restraints weight = 61400.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145511 restraints weight = 67044.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145636 restraints weight = 56445.540| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20733 Z= 0.160 Angle : 0.718 19.621 28365 Z= 0.348 Chirality : 0.048 0.535 3398 Planarity : 0.004 0.043 3456 Dihedral : 9.066 85.095 4276 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.28 % Favored : 93.56 % Rotamer: Outliers : 3.19 % Allowed : 14.51 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.17), residues: 2454 helix: -1.36 (0.25), residues: 378 sheet: -0.09 (0.18), residues: 762 loop : -1.18 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.018 0.001 TYR G 643 PHE 0.011 0.002 PHE K 317 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (20606) covalent geometry : angle 0.67440 (28029) SS BOND : bond 0.00229 ( 45) SS BOND : angle 0.60724 ( 90) hydrogen bonds : bond 0.03883 ( 653) hydrogen bonds : angle 5.50569 ( 1821) link_ALPHA1-2 : bond 0.00850 ( 14) link_ALPHA1-2 : angle 1.85693 ( 42) link_ALPHA1-3 : bond 0.01024 ( 12) link_ALPHA1-3 : angle 1.76899 ( 36) link_ALPHA1-6 : bond 0.00483 ( 14) link_ALPHA1-6 : angle 1.82818 ( 42) link_BETA1-4 : bond 0.00684 ( 27) link_BETA1-4 : angle 2.07200 ( 81) link_NAG-ASN : bond 0.01010 ( 15) link_NAG-ASN : angle 4.90283 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9037 (mtp) cc_final: 0.8725 (mtp) REVERT: A 426 MET cc_start: 0.7269 (tpp) cc_final: 0.6750 (tpp) REVERT: B 534 SER cc_start: 0.7623 (t) cc_final: 0.7159 (m) REVERT: F 348 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6792 (mp0) REVERT: G 530 MET cc_start: 0.7995 (mmm) cc_final: 0.7451 (mtt) REVERT: H 50 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.6310 (p90) REVERT: H 85 SER cc_start: 0.7513 (t) cc_final: 0.7290 (p) REVERT: K 348 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: L 518 VAL cc_start: 0.2190 (OUTLIER) cc_final: 0.1944 (p) REVERT: L 660 LEU cc_start: 0.8351 (tp) cc_final: 0.8131 (tt) REVERT: M 3 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: M 59 ASN cc_start: 0.8938 (t0) cc_final: 0.8715 (t0) outliers start: 68 outliers final: 61 residues processed: 230 average time/residue: 0.1403 time to fit residues: 51.6425 Evaluate side-chains 239 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 173 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 348 GLU Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 518 VAL Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.166972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.161459 restraints weight = 28651.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.150669 restraints weight = 56403.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.147230 restraints weight = 64337.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146741 restraints weight = 74274.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146830 restraints weight = 59808.141| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20733 Z= 0.158 Angle : 0.743 29.921 28365 Z= 0.351 Chirality : 0.048 0.504 3398 Planarity : 0.004 0.041 3456 Dihedral : 8.852 83.650 4276 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.13 % Favored : 94.70 % Rotamer: Outliers : 3.33 % Allowed : 14.69 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.17), residues: 2454 helix: -1.20 (0.26), residues: 369 sheet: -0.10 (0.18), residues: 780 loop : -1.16 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 542 TYR 0.016 0.001 TYR I 51 PHE 0.011 0.002 PHE F 317 TRP 0.015 0.001 TRP H 50 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00368 (20606) covalent geometry : angle 0.66409 (28029) SS BOND : bond 0.00225 ( 45) SS BOND : angle 0.60177 ( 90) hydrogen bonds : bond 0.03866 ( 653) hydrogen bonds : angle 5.45791 ( 1821) link_ALPHA1-2 : bond 0.00840 ( 14) link_ALPHA1-2 : angle 1.82764 ( 42) link_ALPHA1-3 : bond 0.01036 ( 12) link_ALPHA1-3 : angle 1.73549 ( 36) link_ALPHA1-6 : bond 0.00470 ( 14) link_ALPHA1-6 : angle 1.77519 ( 42) link_BETA1-4 : bond 0.00615 ( 27) link_BETA1-4 : angle 1.97700 ( 81) link_NAG-ASN : bond 0.00884 ( 15) link_NAG-ASN : angle 7.58385 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.9007 (mtp) cc_final: 0.8680 (mtp) REVERT: A 426 MET cc_start: 0.7371 (tpp) cc_final: 0.6928 (tpp) REVERT: B 534 SER cc_start: 0.7579 (t) cc_final: 0.7158 (m) REVERT: F 348 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: H 50 TRP cc_start: 0.8161 (OUTLIER) cc_final: 0.6376 (p90) REVERT: L 660 LEU cc_start: 0.8346 (tp) cc_final: 0.8113 (tt) REVERT: M 3 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7904 (pt0) outliers start: 71 outliers final: 62 residues processed: 229 average time/residue: 0.1388 time to fit residues: 51.1819 Evaluate side-chains 236 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 16 GLN Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 176 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.160467 restraints weight = 28692.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.149790 restraints weight = 56064.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146278 restraints weight = 64044.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.145880 restraints weight = 77153.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.145995 restraints weight = 55479.028| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20733 Z= 0.187 Angle : 0.749 20.609 28365 Z= 0.360 Chirality : 0.049 0.486 3398 Planarity : 0.004 0.041 3456 Dihedral : 8.950 85.058 4276 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.52 % Favored : 93.32 % Rotamer: Outliers : 3.15 % Allowed : 15.35 % Favored : 81.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.17), residues: 2454 helix: -1.26 (0.26), residues: 375 sheet: -0.06 (0.18), residues: 768 loop : -1.22 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 542 TYR 0.017 0.002 TYR I 51 PHE 0.012 0.002 PHE F 317 TRP 0.017 0.001 TRP H 50 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00446 (20606) covalent geometry : angle 0.69692 (28029) SS BOND : bond 0.00245 ( 45) SS BOND : angle 0.62062 ( 90) hydrogen bonds : bond 0.04055 ( 653) hydrogen bonds : angle 5.52700 ( 1821) link_ALPHA1-2 : bond 0.00827 ( 14) link_ALPHA1-2 : angle 1.82455 ( 42) link_ALPHA1-3 : bond 0.01022 ( 12) link_ALPHA1-3 : angle 1.77144 ( 36) link_ALPHA1-6 : bond 0.00462 ( 14) link_ALPHA1-6 : angle 1.80322 ( 42) link_BETA1-4 : bond 0.00637 ( 27) link_BETA1-4 : angle 2.12866 ( 81) link_NAG-ASN : bond 0.00919 ( 15) link_NAG-ASN : angle 5.76799 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4908 Ramachandran restraints generated. 2454 Oldfield, 0 Emsley, 2454 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8981 (mtp) cc_final: 0.8663 (mtp) REVERT: A 426 MET cc_start: 0.7450 (tpp) cc_final: 0.6995 (tpp) REVERT: B 534 SER cc_start: 0.7668 (t) cc_final: 0.7306 (m) REVERT: F 348 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: H 50 TRP cc_start: 0.8204 (OUTLIER) cc_final: 0.6406 (p90) REVERT: I 49 MET cc_start: 0.7328 (mmm) cc_final: 0.7068 (mmp) REVERT: L 660 LEU cc_start: 0.8358 (tp) cc_final: 0.8126 (tt) REVERT: M 3 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7849 (pt0) outliers start: 67 outliers final: 61 residues processed: 220 average time/residue: 0.1415 time to fit residues: 49.8580 Evaluate side-chains 235 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 295 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 GLU Chi-restraints excluded: chain F residue 398 THR Chi-restraints excluded: chain F residue 413 THR Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain G residue 612 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain H residue 13 ASN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 50 TRP Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 161 THR Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 295 VAL Chi-restraints excluded: chain K residue 340 ASP Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain K residue 496 VAL Chi-restraints excluded: chain L residue 515 ILE Chi-restraints excluded: chain L residue 612 SER Chi-restraints excluded: chain L residue 641 ILE Chi-restraints excluded: chain L residue 653 GLN Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 21 SER Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain M residue 126 SER Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 236 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 203 optimal weight: 0.0060 chunk 162 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162300 restraints weight = 28684.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151645 restraints weight = 54731.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148114 restraints weight = 57463.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.147759 restraints weight = 60323.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.147986 restraints weight = 58035.015| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 20733 Z= 0.150 Angle : 0.740 21.026 28365 Z= 0.351 Chirality : 0.050 0.742 3398 Planarity : 0.004 0.055 3456 Dihedral : 8.864 81.796 4276 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.93 % Favored : 94.87 % Rotamer: Outliers : 2.96 % Allowed : 15.68 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.17), residues: 2454 helix: -1.08 (0.26), residues: 372 sheet: -0.08 (0.18), residues: 780 loop : -1.14 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 542 TYR 0.017 0.001 TYR I 48 PHE 0.011 0.002 PHE K 383 TRP 0.015 0.001 TRP H 50 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00342 (20606) covalent geometry : angle 0.67782 (28029) SS BOND : bond 0.00214 ( 45) SS BOND : angle 0.60379 ( 90) hydrogen bonds : bond 0.03841 ( 653) hydrogen bonds : angle 5.43093 ( 1821) link_ALPHA1-2 : bond 0.00825 ( 14) link_ALPHA1-2 : angle 1.78052 ( 42) link_ALPHA1-3 : bond 0.01030 ( 12) link_ALPHA1-3 : angle 1.68907 ( 36) link_ALPHA1-6 : bond 0.00497 ( 14) link_ALPHA1-6 : angle 1.82931 ( 42) link_BETA1-4 : bond 0.01016 ( 27) link_BETA1-4 : angle 2.34787 ( 81) link_NAG-ASN : bond 0.00889 ( 15) link_NAG-ASN : angle 6.32667 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2713.21 seconds wall clock time: 48 minutes 18.60 seconds (2898.60 seconds total)