Starting phenix.real_space_refine on Sun Oct 25 21:30:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.map" model { file = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sq1_25376/10_2026/7sq1_25376.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 121 5.16 5 C 11459 2.51 5 N 3049 2.21 5 O 3711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18340 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3467 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "D" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3512 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 423} Chain breaks: 3 Chain: "L" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "H" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "G" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3497 Classifications: {'peptide': 444} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "I" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 845 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 958 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BMA': 1, 'MAN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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 chiralities: 3 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "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 chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" 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 chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 3.84, per 1000 atoms: 0.21 Number of scatterers: 18340 At special positions: 0 Unit cell: (189, 152.88, 123.48, 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 121 16.00 O 3711 8.00 N 3049 7.00 C 11459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS C 501 " distance=2.05 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.16 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.14 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.06 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.22 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.18 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.12 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.26 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 605 " - pdb=" SG CYS G 501 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.08 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.08 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.15 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.10 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.19 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.07 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 "HETATM17708 O5 NAG h 2 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA O 1 " - " MAN O 2 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA O 1 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 625 " " NAG B 704 " - " ASN B 637 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 137 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 295 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 355 " " NAG C 609 " - " ASN C 392 " " NAG C 610 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 625 " " NAG D 704 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 137 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 276 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 339 " " NAG E 608 " - " ASN E 448 " " NAG E 609 " - " ASN E 462 " " NAG F 701 " - " ASN F 611 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 637 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 137 " " NAG G 603 " - " ASN G 197 " " NAG G 604 " - " ASN G 276 " " NAG G 605 " - " ASN G 295 " " NAG G 606 " - " ASN G 301 " " NAG G 607 " - " ASN G 332 " " NAG G 608 " - " ASN G 339 " " NAG G 609 " - " ASN G 392 " " NAG G 610 " - " ASN G 398 " " NAG G 611 " - " ASN G 462 " " NAG J 1 " - " ASN C 133 " " NAG K 1 " - " ASN C 197 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 262 " " NAG P 1 " - " ASN C 301 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN C 386 " " NAG S 1 " - " ASN E 156 " " NAG T 1 " - " ASN E 197 " " NAG U 1 " - " ASN E 234 " " NAG V 1 " - " ASN E 262 " " NAG W 1 " - " ASN E 295 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 355 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 392 " " NAG b 1 " - " ASN E 398 " " NAG c 1 " - " ASN G 133 " " NAG d 1 " - " ASN G 156 " " NAG e 1 " - " ASN G 160 " " NAG f 1 " - " ASN G 234 " " NAG g 1 " - " ASN G 262 " " NAG h 1 " - " ASN G 355 " " NAG i 1 " - " ASN G 386 " " NAG j 1 " - " ASN G 448 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 724.2 milliseconds 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4002 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 42 sheets defined 24.5% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.234A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.629A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.941A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 597 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 removed outlier: 3.801A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.611A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 664 removed outlier: 3.800A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 73 removed outlier: 3.544A pdb=" N HIS C 72 " --> pdb=" O TRP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.813A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.648A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.690A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 571 through 597 Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.743A pdb=" N SER D 615 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.634A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.701A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 650 removed outlier: 3.858A pdb=" N GLN D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 664 removed outlier: 4.092A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 removed outlier: 3.692A pdb=" N HIS E 72 " --> pdb=" O TRP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.717A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52A through 54 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.236A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.750A pdb=" N SER F 534 " --> pdb=" O MET F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.799A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 571 through 597 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.666A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 650 Processing helix chain 'F' and resid 650 through 664 removed outlier: 3.941A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 73 removed outlier: 3.615A pdb=" N HIS G 72 " --> pdb=" O TRP G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 99 through 115 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 354 removed outlier: 3.674A pdb=" N LYS G 351 " --> pdb=" O LYS G 347 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS G 352 " --> pdb=" O GLN G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 475 through 484 removed outlier: 3.532A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 481 " --> pdb=" O ASP G 477 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU G 482 " --> pdb=" O ASN G 478 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.668A pdb=" N TYR A 32 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 52A through 54 Processing helix chain 'A' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'B' and resid 603 through 609 removed outlier: 8.546A pdb=" N CYS B 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR C 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N THR B 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL C 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL B 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.691A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.721A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 92 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AA6, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.360A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.586A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.939A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.981A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.871A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.316A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 302 through 309 removed outlier: 4.730A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.301A pdb=" N CYS D 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR E 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR D 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL D 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.656A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.300A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.446A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.967A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.697A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 302 through 309 removed outlier: 4.736A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.686A pdb=" N MET L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.560A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.113A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.611A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 603 through 609 removed outlier: 8.345A pdb=" N CYS F 604 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N TYR G 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR F 606 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL G 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL F 608 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 45 through 47 removed outlier: 4.241A pdb=" N VAL G 242 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 75 through 76 removed outlier: 3.675A pdb=" N VAL G 75 " --> pdb=" O CYS G 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 92 through 94 Processing sheet with id=AD5, first strand: chain 'G' and resid 130 through 133 removed outlier: 3.544A pdb=" N GLN G 130 " --> pdb=" O SER G 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 181 through 183 Processing sheet with id=AD7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.387A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 259 through 261 removed outlier: 6.383A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 271 through 274 removed outlier: 6.933A pdb=" N THR G 450 " --> pdb=" O LEU G 288 " (cutoff:3.500A) removed outlier: 10.164A pdb=" N THR G 290 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ASN G 448 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N VAL G 292 " --> pdb=" O VAL G 446 " (cutoff:3.500A) removed outlier: 9.982A pdb=" N VAL G 446 " --> pdb=" O VAL G 292 " (cutoff:3.500A) removed outlier: 11.344A pdb=" N ILE G 294 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 10.036A pdb=" N ARG G 444 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 393 " --> pdb=" O PHE G 361 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 304 through 309 removed outlier: 3.555A pdb=" N GLN G 315 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.146A pdb=" N PHE I 98 " --> pdb=" O GLN I 90 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N GLN I 90 " --> pdb=" O PHE I 98 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY I 100 " --> pdb=" O CYS I 88 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS I 88 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 84 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N MET I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TYR I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'A' and resid 10 through 12 removed outlier: 7.100A pdb=" N MET A 34 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.593A pdb=" N TYR A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.87 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3190 1.32 - 1.44: 5014 1.44 - 1.57: 10329 1.57 - 1.70: 2 1.70 - 1.82: 168 Bond restraints: 18703 Sorted by residual: bond pdb=" C1 NAG B 701 " pdb=" C2 NAG B 701 " ideal model delta sigma weight residual 1.532 1.603 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.449 0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB TYR A 32 " pdb=" CG TYR A 32 " ideal model delta sigma weight residual 1.512 1.444 0.068 2.20e-02 2.07e+03 9.65e+00 bond pdb=" CG ASP H 101 " pdb=" OD1 ASP H 101 " ideal model delta sigma weight residual 1.249 1.191 0.058 1.90e-02 2.77e+03 9.29e+00 bond pdb=" CB LEU C 111 " pdb=" CG LEU C 111 " ideal model delta sigma weight residual 1.530 1.470 0.060 2.00e-02 2.50e+03 9.08e+00 ... (remaining 18698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.94: 25368 8.94 - 17.88: 9 17.88 - 26.82: 0 26.82 - 35.76: 0 35.76 - 44.70: 6 Bond angle restraints: 25383 Sorted by residual: angle pdb=" C8 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" N2 NAG G 610 " ideal model delta sigma weight residual 115.06 159.76 -44.70 3.00e+00 1.11e-01 2.22e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" N2 NAG F 701 " ideal model delta sigma weight residual 115.06 159.74 -44.68 3.00e+00 1.11e-01 2.22e+02 angle pdb=" N2 NAG G 610 " pdb=" C7 NAG G 610 " pdb=" O7 NAG G 610 " ideal model delta sigma weight residual 123.46 80.00 43.46 3.00e+00 1.11e-01 2.10e+02 angle pdb=" N2 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 123.46 80.02 43.44 3.00e+00 1.11e-01 2.10e+02 angle pdb=" C8 NAG F 701 " pdb=" C7 NAG F 701 " pdb=" O7 NAG F 701 " ideal model delta sigma weight residual 121.48 79.72 41.76 3.00e+00 1.11e-01 1.94e+02 ... (remaining 25378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 9991 17.46 - 34.91: 303 34.91 - 52.37: 95 52.37 - 69.83: 46 69.83 - 87.29: 20 Dihedral angle restraints: 10455 sinusoidal: 4245 harmonic: 6210 Sorted by residual: dihedral pdb=" CB CYS B 605 " pdb=" SG CYS B 605 " pdb=" SG CYS C 501 " pdb=" CB CYS C 501 " ideal model delta sinusoidal sigma weight residual -86.00 -137.19 51.19 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.76 42.76 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -128.23 42.23 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 10452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.263: 3068 0.263 - 0.527: 29 0.527 - 0.790: 5 0.790 - 1.053: 1 1.053 - 1.317: 1 Chirality restraints: 3104 Sorted by residual: chirality pdb=" C1 MAN O 2 " pdb=" O3 BMA O 1 " pdb=" C2 MAN O 2 " pdb=" O5 MAN O 2 " both_signs ideal model delta sigma weight residual False 2.40 1.08 1.32 2.00e-02 2.50e+03 4.34e+03 chirality pdb=" C1 BMA O 1 " pdb=" O4 NAG N 2 " pdb=" C2 BMA O 1 " pdb=" O5 BMA O 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.15 0.75 2.00e-02 2.50e+03 1.40e+03 chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.30e+02 ... (remaining 3101 not shown) Planarity restraints: 3188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " 0.094 2.00e-02 2.50e+03 9.45e-02 1.12e+02 pdb=" CG ASN B 611 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " -0.142 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 448 " 0.072 2.00e-02 2.50e+03 7.52e-02 7.06e+01 pdb=" CG ASN G 448 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN G 448 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN G 448 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG j 1 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 301 " 0.070 2.00e-02 2.50e+03 7.10e-02 6.31e+01 pdb=" CG ASN G 301 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN G 301 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN G 301 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG G 606 " 0.085 2.00e-02 2.50e+03 ... (remaining 3185 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 59 2.48 - 3.08: 12818 3.08 - 3.69: 24999 3.69 - 4.29: 39321 4.29 - 4.90: 63750 Nonbonded interactions: 140947 Sorted by model distance: nonbonded pdb=" C8 NAG R 2 " pdb=" O3 NAG R 2 " model vdw 1.873 3.460 nonbonded pdb=" O3 NAG E 609 " pdb=" O7 NAG E 609 " model vdw 1.887 3.040 nonbonded pdb=" C8 NAG j 1 " pdb=" O3 NAG j 1 " model vdw 1.887 3.460 nonbonded pdb=" C8 NAG G 606 " pdb=" O3 NAG G 606 " model vdw 1.892 3.460 nonbonded pdb=" O ASN G 398 " pdb=" OD1 ASN G 398 " model vdw 1.900 3.040 ... (remaining 140942 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 'H' } ncs_group { reference = (chain 'B' and resid 520 through 703) selection = (chain 'D' and resid 520 through 703) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 32 through 57 or resid 66 through 504 or resid 602 through \ 610)) selection = (chain 'E' and (resid 32 through 57 or resid 66 through 397 or resid 412 through \ 504 or resid 601 through 609)) selection = (chain 'G' and (resid 32 through 184 or resid 189 through 397 or resid 412 throu \ gh 504 or resid 603 through 611)) } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'U' selection = chain 'f' selection = chain 'g' } 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: 12.600 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: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.050 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 0.013 0.262 18839 Z= 0.731 Angle : 1.559 44.703 25751 Z= 0.903 Chirality : 0.083 1.317 3104 Planarity : 0.005 0.034 3122 Dihedral : 11.325 87.287 6342 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.18 % Favored : 98.77 % Rotamer: Outliers : 0.74 % Allowed : 0.74 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.18), residues: 2113 helix: 0.36 (0.22), residues: 373 sheet: 1.35 (0.19), residues: 605 loop : 2.51 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 54 TYR 0.030 0.004 TYR C 191 PHE 0.025 0.004 PHE I 98 TRP 0.029 0.005 TRP G 479 HIS 0.003 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01201 / 0.65 (18703) covalent geometry : angle 1.48432 / 0.89 (25383) SS BOND : bond 0.07335 / 4.50 ( 37) SS BOND : angle 3.17748 / 2.17 ( 74) hydrogen bonds : bond 0.20495 / 13.54 ( 669) hydrogen bonds : angle 7.66030 / 5.45 ( 1866) Misc. bond : bond 0.26200 / 13.79 ( 1) link_ALPHA1-3 : bond 0.00766 / 0.39 ( 2) link_ALPHA1-3 : angle 6.84489 / 2.62 ( 6) link_BETA1-4 : bond 0.05589 / 3.33 ( 30) link_BETA1-4 : angle 6.20749 / 4.00 ( 90) link_NAG-ASN : bond 0.07211 / 4.77 ( 66) link_NAG-ASN : angle 3.30019 / 2.45 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 364 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 656 ASN cc_start: 0.5924 (m-40) cc_final: 0.5666 (p0) REVERT: C 180 ASP cc_start: 0.8615 (m-30) cc_final: 0.8251 (m-30) REVERT: E 161 MET cc_start: 0.8556 (tpt) cc_final: 0.8274 (tpt) REVERT: E 377 ASN cc_start: 0.8798 (t0) cc_final: 0.8499 (t0) REVERT: L 6 GLN cc_start: 0.6429 (tt0) cc_final: 0.6097 (tt0) REVERT: L 29 VAL cc_start: 0.8189 (m) cc_final: 0.7977 (p) REVERT: L 87 PHE cc_start: 0.8325 (m-80) cc_final: 0.8060 (m-80) REVERT: F 574 LYS cc_start: 0.9063 (mttt) cc_final: 0.8687 (mmtt) REVERT: G 125 LEU cc_start: 0.8615 (mt) cc_final: 0.8140 (tp) REVERT: G 504 ARG cc_start: 0.5583 (mtt180) cc_final: 0.4480 (mmt180) REVERT: A 79 TYR cc_start: 0.7225 (m-80) cc_final: 0.6935 (m-80) outliers start: 14 outliers final: 8 residues processed: 376 average time/residue: 0.1471 time to fit residues: 82.3046 Evaluate side-chains 172 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain G residue 88 ASN Chi-restraints excluded: chain G residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 212, 77] chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS C 195 ASN C 422 GLN C 425 ASN D 540 GLN D 543 ASN D 590 GLN E 195 ASN L 89 GLN H 13 GLN H 100 HIS G 377 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.089989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.075585 restraints weight = 55384.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077679 restraints weight = 33009.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079129 restraints weight = 23273.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.080084 restraints weight = 18188.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.080761 restraints weight = 15365.191| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18839 Z= 0.163 Angle : 1.050 43.483 25751 Z= 0.451 Chirality : 0.053 0.721 3104 Planarity : 0.005 0.068 3122 Dihedral : 5.970 83.452 2325 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Rotamer: Outliers : 1.85 % Allowed : 6.34 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.17), residues: 2113 helix: 1.68 (0.26), residues: 386 sheet: 0.82 (0.19), residues: 578 loop : 1.48 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.017 0.001 TYR A 32 PHE 0.040 0.002 PHE E 53 TRP 0.024 0.001 TRP G 479 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (18703) covalent geometry : angle 1.01425 / 0.44 (25383) SS BOND : bond 0.00384 / 0.23 ( 37) SS BOND : angle 1.44466 / 0.99 ( 74) hydrogen bonds : bond 0.05773 / 3.86 ( 669) hydrogen bonds : angle 5.68682 / 4.02 ( 1866) Misc. bond : bond 0.00165 / 0.09 ( 1) link_ALPHA1-3 : bond 0.01893 / 0.99 ( 2) link_ALPHA1-3 : angle 3.10025 / 1.44 ( 6) link_BETA1-4 : bond 0.00679 / 0.43 ( 30) link_BETA1-4 : angle 1.95247 / 1.26 ( 90) link_NAG-ASN : bond 0.00595 / 0.40 ( 66) link_NAG-ASN : angle 2.93060 / 2.24 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 571 TRP cc_start: 0.6603 (m-10) cc_final: 0.6157 (m-10) REVERT: B 656 ASN cc_start: 0.5712 (m-40) cc_final: 0.5473 (p0) REVERT: C 50 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 180 ASP cc_start: 0.8353 (m-30) cc_final: 0.7969 (m-30) REVERT: E 377 ASN cc_start: 0.8461 (t0) cc_final: 0.8057 (t0) REVERT: E 424 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.8935 (mt) REVERT: L 6 GLN cc_start: 0.6606 (tt0) cc_final: 0.6362 (tt0) REVERT: L 82 ASP cc_start: 0.7867 (m-30) cc_final: 0.7528 (m-30) REVERT: L 87 PHE cc_start: 0.8485 (m-80) cc_final: 0.8283 (m-80) REVERT: L 104 LEU cc_start: 0.8247 (tp) cc_final: 0.7802 (tp) REVERT: F 574 LYS cc_start: 0.8897 (mttt) cc_final: 0.8567 (mmtt) REVERT: G 504 ARG cc_start: 0.5774 (mtt180) cc_final: 0.4381 (mmt180) REVERT: A 29 LEU cc_start: 0.8215 (tp) cc_final: 0.7903 (tt) outliers start: 35 outliers final: 26 residues processed: 219 average time/residue: 0.1231 time to fit residues: 42.5062 Evaluate side-chains 194 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain I residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [11, 92, 187, 172, 6, 66, 120, 82, 209, 153, 196] chunk 11 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 187 optimal weight: 0.0970 chunk 172 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 120 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 616 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 136 ASN L 38 GLN L 53 ASN L 89 GLN H 39 GLN H 100 HIS ** F 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 658 GLN G 105 HIS G 330 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.082261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067641 restraints weight = 58112.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069534 restraints weight = 35537.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.070829 restraints weight = 25538.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071693 restraints weight = 20388.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.072240 restraints weight = 17477.925| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 18839 Z= 0.278 Angle : 1.084 43.674 25751 Z= 0.472 Chirality : 0.053 0.623 3104 Planarity : 0.006 0.076 3122 Dihedral : 6.133 79.861 2319 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.11 % Rotamer: Outliers : 3.01 % Allowed : 6.76 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.17), residues: 2113 helix: 1.22 (0.26), residues: 392 sheet: 0.47 (0.20), residues: 600 loop : 0.49 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 94 TYR 0.019 0.002 TYR I 49 PHE 0.031 0.003 PHE E 53 TRP 0.019 0.002 TRP D 623 HIS 0.054 0.003 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.28 (18703) covalent geometry : angle 1.04811 / 0.46 (25383) SS BOND : bond 0.00923 / 0.69 ( 37) SS BOND : angle 1.92907 / 1.39 ( 74) hydrogen bonds : bond 0.05405 / 3.58 ( 669) hydrogen bonds : angle 5.53122 / 3.90 ( 1866) Misc. bond : bond 0.00112 / 0.06 ( 1) link_ALPHA1-3 : bond 0.00162 / 0.08 ( 2) link_ALPHA1-3 : angle 3.12033 / 1.31 ( 6) link_BETA1-4 : bond 0.00671 / 0.46 ( 30) link_BETA1-4 : angle 2.01200 / 1.35 ( 90) link_NAG-ASN : bond 0.00597 / 0.40 ( 66) link_NAG-ASN : angle 2.91970 / 2.15 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: E 377 ASN cc_start: 0.8606 (t0) cc_final: 0.8275 (t0) REVERT: E 424 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9232 (mt) REVERT: L 29 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7962 (t) REVERT: F 574 LYS cc_start: 0.8927 (mttt) cc_final: 0.8546 (mmtt) REVERT: G 301 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7792 (t0) REVERT: G 426 MET cc_start: 0.7279 (mtp) cc_final: 0.6939 (mtp) REVERT: G 504 ARG cc_start: 0.5779 (mtt180) cc_final: 0.4488 (mmt180) outliers start: 57 outliers final: 43 residues processed: 196 average time/residue: 0.1231 time to fit residues: 38.1433 Evaluate side-chains 183 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 424 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [166, 127, 85, 82, 86, 172, 193, 156, 180, 33, 145] chunk 166 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN E 195 ASN F 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.083998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.069454 restraints weight = 57123.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071388 restraints weight = 34660.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072667 restraints weight = 24758.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073573 restraints weight = 19833.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074203 restraints weight = 16882.587| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18839 Z= 0.134 Angle : 0.952 43.461 25751 Z= 0.396 Chirality : 0.048 0.479 3104 Planarity : 0.004 0.057 3122 Dihedral : 5.661 79.136 2317 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.26 % Rotamer: Outliers : 2.38 % Allowed : 7.71 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.17), residues: 2113 helix: 1.44 (0.27), residues: 398 sheet: 0.46 (0.20), residues: 583 loop : 0.33 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 18 TYR 0.014 0.001 TYR B 643 PHE 0.029 0.002 PHE E 53 TRP 0.014 0.001 TRP B 610 HIS 0.006 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (18703) covalent geometry : angle 0.92130 / 0.39 (25383) SS BOND : bond 0.00480 / 0.30 ( 37) SS BOND : angle 1.48320 / 1.10 ( 74) hydrogen bonds : bond 0.04236 / 2.81 ( 669) hydrogen bonds : angle 5.18584 / 3.64 ( 1866) Misc. bond : bond 0.00027 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00848 / 0.44 ( 2) link_ALPHA1-3 : angle 2.56130 / 1.09 ( 6) link_BETA1-4 : bond 0.00566 / 0.37 ( 30) link_BETA1-4 : angle 1.79325 / 1.18 ( 90) link_NAG-ASN : bond 0.00415 / 0.28 ( 66) link_NAG-ASN : angle 2.56201 / 1.93 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 180 ASP cc_start: 0.8408 (m-30) cc_final: 0.8185 (m-30) REVERT: D 540 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: E 377 ASN cc_start: 0.8530 (t0) cc_final: 0.8263 (t0) REVERT: L 29 VAL cc_start: 0.8144 (OUTLIER) cc_final: 0.7922 (t) REVERT: L 102 THR cc_start: 0.7594 (m) cc_final: 0.7304 (p) REVERT: F 574 LYS cc_start: 0.8872 (mttt) cc_final: 0.8483 (mmtt) REVERT: F 633 LYS cc_start: 0.9013 (pttp) cc_final: 0.8439 (mttp) REVERT: G 301 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7892 (t0) REVERT: G 376 PHE cc_start: 0.8155 (m-80) cc_final: 0.7877 (m-10) REVERT: G 504 ARG cc_start: 0.5766 (mtt180) cc_final: 0.4501 (mmt180) REVERT: A 18 MET cc_start: 0.5803 (ttm) cc_final: 0.5388 (ttt) outliers start: 45 outliers final: 32 residues processed: 186 average time/residue: 0.1209 time to fit residues: 36.2996 Evaluate side-chains 171 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 301 ASN Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Chi-restraints excluded: chain A residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [64, 148, 178, 81, 212, 58, 111, 78, 31, 92, 93] chunk 64 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 422 GLN E 136 ASN E 249 HIS L 76 HIS F 590 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.065190 restraints weight = 58431.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066946 restraints weight = 36752.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068145 restraints weight = 26866.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068964 restraints weight = 21712.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069517 restraints weight = 18728.974| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18839 Z= 0.274 Angle : 1.060 43.754 25751 Z= 0.456 Chirality : 0.052 0.416 3104 Planarity : 0.005 0.079 3122 Dihedral : 6.109 86.123 2317 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 3.01 % Allowed : 8.40 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.17), residues: 2113 helix: 1.14 (0.26), residues: 398 sheet: 0.25 (0.20), residues: 588 loop : -0.25 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.021 0.002 TYR H 98 PHE 0.027 0.003 PHE E 376 TRP 0.015 0.002 TRP A 33 HIS 0.032 0.002 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 (18703) covalent geometry : angle 1.02797 / 0.45 (25383) SS BOND : bond 0.00466 / 0.29 ( 37) SS BOND : angle 1.53650 / 1.11 ( 74) hydrogen bonds : bond 0.05208 / 3.48 ( 669) hydrogen bonds : angle 5.45552 / 3.83 ( 1866) Misc. bond : bond 0.00149 / 0.08 ( 1) link_ALPHA1-3 : bond 0.00728 / 0.38 ( 2) link_ALPHA1-3 : angle 2.16983 / 1.02 ( 6) link_BETA1-4 : bond 0.00518 / 0.34 ( 30) link_BETA1-4 : angle 1.92790 / 1.28 ( 90) link_NAG-ASN : bond 0.00529 / 0.36 ( 66) link_NAG-ASN : angle 2.81843 / 2.05 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7587 (mp10) REVERT: E 377 ASN cc_start: 0.8630 (t0) cc_final: 0.8344 (t0) REVERT: L 78 MET cc_start: 0.7895 (tpt) cc_final: 0.7239 (tpt) REVERT: L 80 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7447 (tm-30) REVERT: H 32 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6047 (t80) REVERT: F 633 LYS cc_start: 0.9059 (pttp) cc_final: 0.8372 (mttt) REVERT: G 504 ARG cc_start: 0.5983 (mtt180) cc_final: 0.4652 (mmt180) REVERT: A 33 TRP cc_start: 0.6965 (OUTLIER) cc_final: 0.6576 (t60) REVERT: A 82 ASN cc_start: 0.8653 (t0) cc_final: 0.8435 (t0) outliers start: 57 outliers final: 44 residues processed: 185 average time/residue: 0.1318 time to fit residues: 38.2887 Evaluate side-chains 177 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 136 ASN Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [116, 27, 84, 53, 69, 111, 204, 3, 184, 148, 0] chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 204 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS L 6 GLN F 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.081022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066687 restraints weight = 57460.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068495 restraints weight = 35707.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.069735 restraints weight = 25847.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070589 restraints weight = 20707.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.071149 restraints weight = 17765.088| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18839 Z= 0.159 Angle : 0.967 43.490 25751 Z= 0.402 Chirality : 0.048 0.385 3104 Planarity : 0.004 0.053 3122 Dihedral : 5.750 87.853 2315 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 2.59 % Allowed : 9.77 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2113 helix: 1.33 (0.26), residues: 401 sheet: 0.28 (0.21), residues: 567 loop : -0.21 (0.17), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 308 TYR 0.014 0.001 TYR A 32 PHE 0.026 0.002 PHE E 53 TRP 0.014 0.001 TRP B 610 HIS 0.006 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (18703) covalent geometry : angle 0.93808 / 0.39 (25383) SS BOND : bond 0.00347 / 0.23 ( 37) SS BOND : angle 1.22175 / 0.89 ( 74) hydrogen bonds : bond 0.04345 / 2.89 ( 669) hydrogen bonds : angle 5.16926 / 3.63 ( 1866) Misc. bond : bond 0.00062 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00677 / 0.35 ( 2) link_ALPHA1-3 : angle 2.10005 / 0.97 ( 6) link_BETA1-4 : bond 0.00535 / 0.35 ( 30) link_BETA1-4 : angle 1.71004 / 1.13 ( 90) link_NAG-ASN : bond 0.00403 / 0.27 ( 66) link_NAG-ASN : angle 2.60924 / 1.94 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 135 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 540 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7657 (mp10) REVERT: E 307 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8576 (pt) REVERT: E 377 ASN cc_start: 0.8555 (t0) cc_final: 0.8323 (t0) REVERT: L 78 MET cc_start: 0.7747 (tpt) cc_final: 0.7189 (tpt) REVERT: L 80 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7429 (tm-30) REVERT: H 32 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.4685 (t80) REVERT: H 75 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8537 (mtm-85) REVERT: F 633 LYS cc_start: 0.9022 (pttp) cc_final: 0.8381 (mttp) REVERT: G 376 PHE cc_start: 0.8233 (m-80) cc_final: 0.7965 (m-10) REVERT: G 504 ARG cc_start: 0.5973 (mtt180) cc_final: 0.4669 (mmt180) REVERT: A 82 ASN cc_start: 0.8701 (t0) cc_final: 0.8468 (t0) outliers start: 49 outliers final: 37 residues processed: 172 average time/residue: 0.1222 time to fit residues: 33.4065 Evaluate side-chains 170 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 290 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 398 ASN Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [17, 130, 126, 32, 15, 61, 33, 74, 119, 47, 174] chunk 17 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 15 optimal weight: 0.0270 chunk 61 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 174 optimal weight: 8.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.3625 r_free = 0.3625 target = 0.083109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.068762 restraints weight = 56926.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.070646 restraints weight = 35084.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071937 restraints weight = 25181.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072725 restraints weight = 20076.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.073358 restraints weight = 17305.394| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18839 Z= 0.105 Angle : 0.922 43.397 25751 Z= 0.375 Chirality : 0.047 0.383 3104 Planarity : 0.004 0.054 3122 Dihedral : 5.410 87.493 2315 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 2.01 % Allowed : 10.25 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2113 helix: 1.69 (0.27), residues: 395 sheet: 0.36 (0.21), residues: 573 loop : -0.09 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 75 TYR 0.012 0.001 TYR F 586 PHE 0.027 0.001 PHE E 53 TRP 0.014 0.001 TRP H 103 HIS 0.014 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (18703) covalent geometry : angle 0.89693 / 0.37 (25383) SS BOND : bond 0.00273 / 0.19 ( 37) SS BOND : angle 1.02723 / 0.73 ( 74) hydrogen bonds : bond 0.03618 / 2.41 ( 669) hydrogen bonds : angle 4.85277 / 3.40 ( 1866) Misc. bond : bond 0.00007 / 0.00 ( 1) link_ALPHA1-3 : bond 0.00794 / 0.40 ( 2) link_ALPHA1-3 : angle 2.04685 / 0.95 ( 6) link_BETA1-4 : bond 0.00556 / 0.36 ( 30) link_BETA1-4 : angle 1.56518 / 1.04 ( 90) link_NAG-ASN : bond 0.00433 / 0.29 ( 66) link_NAG-ASN : angle 2.38689 / 1.79 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 142 MET cc_start: 0.2572 (mmm) cc_final: 0.0438 (ttt) REVERT: D 540 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.5816 (mp-120) REVERT: E 307 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8543 (pt) REVERT: L 78 MET cc_start: 0.7565 (tpt) cc_final: 0.7188 (tpt) REVERT: H 32 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4195 (t80) REVERT: H 75 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8384 (mtm180) REVERT: F 633 LYS cc_start: 0.9026 (pttp) cc_final: 0.8421 (mttp) REVERT: G 504 ARG cc_start: 0.5997 (mtt180) cc_final: 0.4674 (mmt180) REVERT: A 5 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6518 (mp0) REVERT: A 82 ASN cc_start: 0.8674 (t0) cc_final: 0.8347 (t0) outliers start: 38 outliers final: 27 residues processed: 170 average time/residue: 0.1254 time to fit residues: 33.9343 Evaluate side-chains 158 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 75 ARG Chi-restraints excluded: chain G residue 137 ASN Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [94, 97, 104, 193, 185, 130, 7, 46, 124, 20, 122] chunk 94 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 0.0370 chunk 124 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 122 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069094 restraints weight = 56508.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070954 restraints weight = 34789.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072230 restraints weight = 25059.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073099 restraints weight = 20025.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073695 restraints weight = 17097.428| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 18839 Z= 0.107 Angle : 0.918 43.383 25751 Z= 0.373 Chirality : 0.046 0.367 3104 Planarity : 0.004 0.049 3122 Dihedral : 5.259 88.155 2315 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 1.95 % Allowed : 10.57 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2113 helix: 1.72 (0.27), residues: 401 sheet: 0.48 (0.21), residues: 567 loop : -0.08 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.011 0.001 TYR A 32 PHE 0.024 0.001 PHE E 53 TRP 0.013 0.001 TRP A 47 HIS 0.005 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (18703) covalent geometry : angle 0.89605 / 0.37 (25383) SS BOND : bond 0.00280 / 0.19 ( 37) SS BOND : angle 1.25834 / 0.95 ( 74) hydrogen bonds : bond 0.03448 / 2.28 ( 669) hydrogen bonds : angle 4.73194 / 3.31 ( 1866) Misc. bond : bond 0.00032 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00770 / 0.39 ( 2) link_ALPHA1-3 : angle 2.05481 / 0.94 ( 6) link_BETA1-4 : bond 0.00510 / 0.33 ( 30) link_BETA1-4 : angle 1.50958 / 1.02 ( 90) link_NAG-ASN : bond 0.00426 / 0.28 ( 66) link_NAG-ASN : angle 2.19478 / 1.64 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7612 (mmm) cc_final: 0.7318 (mmt) REVERT: B 656 ASN cc_start: 0.5536 (m-40) cc_final: 0.4993 (p0) REVERT: D 540 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.5914 (mp-120) REVERT: D 633 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8706 (pptt) REVERT: E 307 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8581 (pt) REVERT: L 78 MET cc_start: 0.7442 (tpt) cc_final: 0.7111 (tpt) REVERT: L 97 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (m) REVERT: H 32 TYR cc_start: 0.5746 (OUTLIER) cc_final: 0.4387 (t80) REVERT: F 574 LYS cc_start: 0.8790 (mttt) cc_final: 0.8314 (mmtt) REVERT: F 633 LYS cc_start: 0.9004 (pttp) cc_final: 0.8404 (mttt) REVERT: G 504 ARG cc_start: 0.6088 (mtt180) cc_final: 0.4699 (mmt180) REVERT: I 3 VAL cc_start: 0.8517 (t) cc_final: 0.8202 (m) REVERT: A 5 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6487 (mp0) REVERT: A 43 LYS cc_start: 0.7510 (mttt) cc_final: 0.7113 (pttm) REVERT: A 82 ASN cc_start: 0.8689 (t0) cc_final: 0.8393 (t0) outliers start: 37 outliers final: 27 residues processed: 167 average time/residue: 0.1240 time to fit residues: 32.5591 Evaluate side-chains 164 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [14, 209, 58, 113, 211, 92, 12, 79, 76, 54, 206] chunk 14 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.068056 restraints weight = 57125.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069903 restraints weight = 34802.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071224 restraints weight = 25026.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072115 restraints weight = 19852.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072712 restraints weight = 16899.258| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18839 Z= 0.131 Angle : 0.927 43.430 25751 Z= 0.379 Chirality : 0.047 0.357 3104 Planarity : 0.004 0.052 3122 Dihedral : 5.268 89.581 2315 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.55 % Favored : 96.40 % Rotamer: Outliers : 1.80 % Allowed : 11.15 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2113 helix: 1.70 (0.27), residues: 401 sheet: 0.50 (0.21), residues: 568 loop : -0.12 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 75 TYR 0.018 0.001 TYR B 643 PHE 0.023 0.001 PHE E 53 TRP 0.011 0.001 TRP A 33 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (18703) covalent geometry : angle 0.90571 / 0.37 (25383) SS BOND : bond 0.00313 / 0.21 ( 37) SS BOND : angle 1.29449 / 0.98 ( 74) hydrogen bonds : bond 0.03558 / 2.35 ( 669) hydrogen bonds : angle 4.73090 / 3.32 ( 1866) Misc. bond : bond 0.00054 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00745 / 0.38 ( 2) link_ALPHA1-3 : angle 2.09519 / 0.96 ( 6) link_BETA1-4 : bond 0.00498 / 0.33 ( 30) link_BETA1-4 : angle 1.51905 / 1.02 ( 90) link_NAG-ASN : bond 0.00383 / 0.25 ( 66) link_NAG-ASN : angle 2.19131 / 1.63 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 137 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7686 (mmm) cc_final: 0.7326 (mmt) REVERT: B 656 ASN cc_start: 0.5553 (m-40) cc_final: 0.5001 (p0) REVERT: C 142 MET cc_start: 0.2675 (mmm) cc_final: 0.0513 (ttt) REVERT: D 540 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: D 633 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8689 (pptt) REVERT: E 307 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8589 (pt) REVERT: E 430 ILE cc_start: 0.8453 (mm) cc_final: 0.8150 (mp) REVERT: L 78 MET cc_start: 0.7477 (tpt) cc_final: 0.7149 (tpt) REVERT: L 97 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (m) REVERT: H 32 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.4529 (t80) REVERT: F 574 LYS cc_start: 0.8812 (mttt) cc_final: 0.8337 (mmtt) REVERT: F 633 LYS cc_start: 0.9008 (pttp) cc_final: 0.8384 (mttt) REVERT: G 504 ARG cc_start: 0.6103 (mtt180) cc_final: 0.4735 (mmt180) REVERT: A 5 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6554 (mp0) REVERT: A 43 LYS cc_start: 0.7573 (mttt) cc_final: 0.7189 (pttm) REVERT: A 82 ASN cc_start: 0.8696 (t0) cc_final: 0.8400 (t0) outliers start: 34 outliers final: 28 residues processed: 160 average time/residue: 0.1264 time to fit residues: 32.2345 Evaluate side-chains 168 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [162, 192, 106, 195, 83, 89, 22, 5, 98, 198, 138] chunk 162 optimal weight: 7.9990 chunk 192 optimal weight: 0.0670 chunk 106 optimal weight: 0.9980 chunk 195 optimal weight: 0.0060 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 5 optimal weight: 0.1980 chunk 98 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.083587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.069440 restraints weight = 56647.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.071290 restraints weight = 34614.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.072576 restraints weight = 24829.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073450 restraints weight = 19724.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073975 restraints weight = 16835.211| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 18839 Z= 0.103 Angle : 0.915 43.372 25751 Z= 0.372 Chirality : 0.046 0.350 3104 Planarity : 0.004 0.048 3122 Dihedral : 5.180 89.884 2315 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 11.52 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2113 helix: 1.86 (0.27), residues: 401 sheet: 0.52 (0.21), residues: 572 loop : -0.12 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 308 TYR 0.013 0.001 TYR B 643 PHE 0.023 0.001 PHE E 53 TRP 0.011 0.001 TRP A 47 HIS 0.010 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (18703) covalent geometry : angle 0.89578 / 0.37 (25383) SS BOND : bond 0.00277 / 0.19 ( 37) SS BOND : angle 1.21816 / 0.92 ( 74) hydrogen bonds : bond 0.03311 / 2.19 ( 669) hydrogen bonds : angle 4.62892 / 3.25 ( 1866) Misc. bond : bond 0.00023 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00782 / 0.40 ( 2) link_ALPHA1-3 : angle 2.07506 / 0.96 ( 6) link_BETA1-4 : bond 0.00528 / 0.34 ( 30) link_BETA1-4 : angle 1.47992 / 0.99 ( 90) link_NAG-ASN : bond 0.00396 / 0.26 ( 66) link_NAG-ASN : angle 2.09901 / 1.58 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4226 Ramachandran restraints generated. 2113 Oldfield, 0 Emsley, 2113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7637 (mmm) cc_final: 0.7307 (mmt) REVERT: B 656 ASN cc_start: 0.5624 (m-40) cc_final: 0.5094 (p0) REVERT: C 142 MET cc_start: 0.2554 (mmm) cc_final: 0.0455 (ttt) REVERT: D 540 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.5955 (mp-120) REVERT: D 633 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8695 (pptt) REVERT: E 430 ILE cc_start: 0.8425 (mm) cc_final: 0.8117 (mp) REVERT: L 97 THR cc_start: 0.8451 (m) cc_final: 0.8220 (m) REVERT: H 32 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.4375 (t80) REVERT: F 574 LYS cc_start: 0.8717 (mttt) cc_final: 0.8291 (mmtt) REVERT: F 633 LYS cc_start: 0.8997 (pttp) cc_final: 0.8407 (mttp) REVERT: G 125 LEU cc_start: 0.8915 (tp) cc_final: 0.8326 (tp) REVERT: G 504 ARG cc_start: 0.6131 (mtt180) cc_final: 0.4752 (mmt180) REVERT: I 24 ARG cc_start: 0.7889 (ptm-80) cc_final: 0.7595 (ptm-80) REVERT: A 43 LYS cc_start: 0.7633 (mttt) cc_final: 0.7224 (pttm) REVERT: A 77 THR cc_start: 0.7466 (p) cc_final: 0.7061 (p) REVERT: A 82 ASN cc_start: 0.8690 (t0) cc_final: 0.8410 (t0) outliers start: 30 outliers final: 27 residues processed: 166 average time/residue: 0.1229 time to fit residues: 32.8637 Evaluate side-chains 167 residues out of total 1893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 633 LYS Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 398 ASN Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 88 CYS Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain A residue 33 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: [149, 182, 178, 151, 122, 32, 140, 24, 35, 16, 143] chunk 149 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 143 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** 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 = 0.3618 r_free = 0.3618 target = 0.082731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068477 restraints weight = 56854.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070311 restraints weight = 35028.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071577 restraints weight = 25215.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.072456 restraints weight = 20108.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.072971 restraints weight = 17137.197| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18839 Z= 0.121 Angle : 0.921 43.407 25751 Z= 0.376 Chirality : 0.047 0.341 3104 Planarity : 0.004 0.052 3122 Dihedral : 5.181 88.329 2315 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 2.11 % Allowed : 11.09 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2113 helix: 1.80 (0.27), residues: 401 sheet: 0.56 (0.21), residues: 568 loop : -0.13 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 308 TYR 0.011 0.001 TYR B 643 PHE 0.022 0.001 PHE E 53 TRP 0.010 0.001 TRP A 33 HIS 0.008 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18703) covalent geometry : angle 0.90120 / 0.37 (25383) SS BOND : bond 0.00299 / 0.20 ( 37) SS BOND : angle 1.21978 / 0.92 ( 74) hydrogen bonds : bond 0.03448 / 2.27 ( 669) hydrogen bonds : angle 4.64163 / 3.26 ( 1866) Misc. bond : bond 0.00053 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00752 / 0.38 ( 2) link_ALPHA1-3 : angle 2.09551 / 0.97 ( 6) link_BETA1-4 : bond 0.00496 / 0.32 ( 30) link_BETA1-4 : angle 1.49290 / 1.00 ( 90) link_NAG-ASN : bond 0.00379 / 0.25 ( 66) link_NAG-ASN : angle 2.10893 / 1.57 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.84 seconds wall clock time: 50 minutes 26.30 seconds (3026.30 seconds total)