Starting phenix.real_space_refine on Sun Jul 5 13:41:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ymz_33948/07_2026/7ymz_33948.cif" } resolution = 4.39 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= -0.005 sd= 0.116 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 153 5.16 5 C 17670 2.51 5 N 4515 2.21 5 O 5553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27891 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "K" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "A" 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: "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: 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 Time building chain proxies: 6.51, per 1000 atoms: 0.23 Number of scatterers: 27891 At special positions: 0 Unit cell: (152.9, 146.3, 160.6, 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 153 16.00 O 5553 8.00 N 4515 7.00 C 17670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 2 " " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " NAG-ASN " NAG A1401 " - " ASN A 166 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 785 " " NAG B1401 " - " ASN B 166 " " NAG B1402 " - " ASN B 785 " " NAG B1403 " - " ASN B 236 " " NAG B1404 " - " ASN B 244 " " NAG C1401 " - " ASN C 244 " " NAG C1402 " - " ASN C 785 " " NAG C1403 " - " ASN C 236 " " NAG C1404 " - " ASN C 166 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN A 619 " " NAG H 1 " - " ASN A 719 " " NAG I 1 " - " ASN A 870 " " NAG J 1 " - " ASN A1213 " " NAG K 1 " - " ASN B 719 " " NAG L 1 " - " ASN B 870 " " NAG M 1 " - " ASN B 125 " " NAG N 1 " - " ASN B1213 " " NAG O 1 " - " ASN B 619 " " NAG P 1 " - " ASN B 222 " " NAG Q 1 " - " ASN B 66 " " NAG R 1 " - " ASN C 125 " " NAG S 1 " - " ASN C 619 " " NAG T 1 " - " ASN C 719 " " NAG U 1 " - " ASN C 222 " " NAG V 1 " - " ASN C 870 " " NAG W 1 " - " ASN C 66 " " NAG X 1 " - " ASN C1213 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.3 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 56 sheets defined 25.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.462A pdb=" N SER A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.810A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.258A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.238A pdb=" N ILE A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.675A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.607A pdb=" N GLU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 853 Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.938A pdb=" N GLN A 927 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 929 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 956 removed outlier: 3.823A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 removed outlier: 3.566A pdb=" N SER A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1010 removed outlier: 3.680A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.539A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.116A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.791A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.520A pdb=" N GLN B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.837A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.877A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.880A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.864A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 825 through 853 removed outlier: 4.379A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.576A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.903A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.560A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.780A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.581A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.741A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.602A pdb=" N SER C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.725A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.577A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.789A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 430 through 436 removed outlier: 4.339A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 4.145A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.610A pdb=" N ILE C 529 " --> pdb=" O CYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 823 removed outlier: 4.155A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 908 through 915 Processing helix chain 'C' and resid 925 through 930 removed outlier: 4.141A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 958 removed outlier: 4.116A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 removed outlier: 3.769A pdb=" N GLY C 984 " --> pdb=" O LEU C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.814A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1011 removed outlier: 4.300A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.863A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 4.325A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.514A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.676A pdb=" N TYR A 85 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.573A pdb=" N THR A 93 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 96 " --> pdb=" O THR A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.650A pdb=" N LYS A 110 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 293 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 removed outlier: 5.853A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.252A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.940A pdb=" N VAL A 374 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.655A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.094A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 504 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.808A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 769 removed outlier: 6.024A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 782 removed outlier: 4.466A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 795 removed outlier: 6.669A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN A1129 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.955A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.444A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.509A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 280 through 284 removed outlier: 4.817A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 155 removed outlier: 5.482A pdb=" N GLY B 154 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.931A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.642A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE B 630 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.654A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AD2, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.911A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 723 through 724 removed outlier: 3.740A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 768 through 769 removed outlier: 6.417A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.803A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 802 through 803 Processing sheet with id=AD8, first strand: chain 'B' and resid 1155 through 1157 Processing sheet with id=AD9, first strand: chain 'B' and resid 1165 through 1167 Processing sheet with id=AE1, first strand: chain 'B' and resid 1173 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.400A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.903A pdb=" N THR C 93 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 96 " --> pdb=" O THR C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.774A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.555A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 119 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR C 314 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.605A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE8, first strand: chain 'C' and resid 359 through 362 removed outlier: 4.198A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.875A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.988A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.031A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 617 through 618 removed outlier: 4.481A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 718 removed outlier: 6.336A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 717 through 718 removed outlier: 6.336A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 758 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 778 through 782 Processing sheet with id=AF8, first strand: chain 'C' and resid 785 through 796 removed outlier: 6.697A pdb=" N GLY C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN C1129 " --> pdb=" O GLY C1133 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR C1135 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C1127 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET C1137 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER C1125 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1139 " --> pdb=" O ILE C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AG1, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.810A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS C1156 " --> pdb=" O ILE C1214 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1170 through 1174 removed outlier: 4.504A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 2712 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: 7.25 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4515 1.30 - 1.44: 8044 1.44 - 1.57: 15757 1.57 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 28521 Sorted by residual: bond pdb=" CA GLU C 252 " pdb=" C GLU C 252 " ideal model delta sigma weight residual 1.521 1.442 0.079 1.17e-02 7.31e+03 4.60e+01 bond pdb=" CA PHE A1019 " pdb=" C PHE A1019 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.35e-02 5.49e+03 4.02e+01 bond pdb=" CA SER A 106 " pdb=" C SER A 106 " ideal model delta sigma weight residual 1.525 1.439 0.086 1.37e-02 5.33e+03 3.93e+01 bond pdb=" C GLU C 252 " pdb=" O GLU C 252 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.14e-02 7.69e+03 3.90e+01 bond pdb=" CA VAL A1022 " pdb=" C VAL A1022 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.23e-02 6.61e+03 3.74e+01 ... (remaining 28516 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 38082 2.83 - 5.66: 619 5.66 - 8.50: 80 8.50 - 11.33: 19 11.33 - 14.16: 2 Bond angle restraints: 38802 Sorted by residual: angle pdb=" N VAL A1022 " pdb=" CA VAL A1022 " pdb=" C VAL A1022 " ideal model delta sigma weight residual 110.53 102.38 8.15 9.40e-01 1.13e+00 7.51e+01 angle pdb=" N ARG B 235 " pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 108.34 118.52 -10.18 1.31e+00 5.83e-01 6.04e+01 angle pdb=" N PHE A1019 " pdb=" CA PHE A1019 " pdb=" C PHE A1019 " ideal model delta sigma weight residual 111.82 103.30 8.52 1.16e+00 7.43e-01 5.39e+01 angle pdb=" N PHE B 399 " pdb=" CA PHE B 399 " pdb=" C PHE B 399 " ideal model delta sigma weight residual 108.67 118.58 -9.91 1.55e+00 4.16e-01 4.09e+01 angle pdb=" N LEU B 234 " pdb=" CA LEU B 234 " pdb=" C LEU B 234 " ideal model delta sigma weight residual 108.90 118.77 -9.87 1.63e+00 3.76e-01 3.67e+01 ... (remaining 38797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 14859 17.94 - 35.89: 1318 35.89 - 53.83: 242 53.83 - 71.77: 71 71.77 - 89.72: 40 Dihedral angle restraints: 16530 sinusoidal: 6339 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -167.74 81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS C1106 " pdb=" SG CYS C1106 " pdb=" SG CYS C1117 " pdb=" CB CYS C1117 " ideal model delta sinusoidal sigma weight residual 93.00 168.11 -75.11 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.07 74.07 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4439 0.148 - 0.296: 77 0.296 - 0.444: 8 0.444 - 0.592: 1 0.592 - 0.740: 2 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 125 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4524 not shown) Planarity restraints: 4977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " 0.037 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" CG ASN A 222 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 221 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG A 221 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG A 221 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 222 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 397 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 397 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR B 397 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 398 " 0.019 2.00e-02 2.50e+03 ... (remaining 4974 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2199 2.74 - 3.28: 27685 3.28 - 3.82: 48607 3.82 - 4.36: 53735 4.36 - 4.90: 90464 Nonbonded interactions: 222690 Sorted by model distance: nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.199 3.040 nonbonded pdb=" O PHE C 399 " pdb=" OH TYR C 523 " model vdw 2.199 3.040 nonbonded pdb=" OH TYR C 824 " pdb=" OD1 ASP C1068 " model vdw 2.231 3.040 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.240 3.040 nonbonded pdb=" OG SER A 268 " pdb=" O ASP A 272 " model vdw 2.250 3.040 ... (remaining 222685 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.290 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 28632 Z= 0.280 Angle : 0.934 24.584 39087 Z= 0.476 Chirality : 0.059 0.740 4527 Planarity : 0.006 0.079 4944 Dihedral : 14.782 89.717 9876 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.41 % Favored : 93.39 % Rotamer: Outliers : 0.70 % Allowed : 0.63 % Favored : 98.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.14), residues: 3462 helix: -0.08 (0.19), residues: 691 sheet: -0.34 (0.19), residues: 702 loop : -1.47 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 505 TYR 0.027 0.002 TYR C 71 PHE 0.038 0.002 PHE A 254 TRP 0.021 0.001 TRP C 253 HIS 0.010 0.001 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.28 (28521) covalent geometry : angle 0.89156 / 0.47 (38802) SS BOND : bond 0.00209 / 0.15 ( 48) SS BOND : angle 1.45948 / 0.85 ( 96) hydrogen bonds : bond 0.14178 / 9.02 ( 1021) hydrogen bonds : angle 6.93291 / 4.92 ( 2712) link_ALPHA1-3 : bond 0.00256 / 0.12 ( 3) link_ALPHA1-3 : angle 1.93181 / 1.06 ( 9) link_ALPHA1-6 : bond 0.00311 / 0.12 ( 3) link_ALPHA1-6 : angle 1.66194 / 0.84 ( 9) link_BETA1-4 : bond 0.01096 / 0.80 ( 18) link_BETA1-4 : angle 3.54134 / 2.35 ( 54) link_BETA1-6 : bond 0.01226 / 0.64 ( 6) link_BETA1-6 : angle 2.87567 / 1.88 ( 18) link_NAG-ASN : bond 0.01182 / 0.80 ( 33) link_NAG-ASN : angle 4.69761 / 2.97 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7812 (mmt) cc_final: 0.7572 (mmm) REVERT: A 296 ILE cc_start: 0.8920 (mp) cc_final: 0.8676 (mp) REVERT: A 452 MET cc_start: 0.7393 (pmm) cc_final: 0.7044 (pmm) REVERT: A 563 MET cc_start: 0.8976 (tpt) cc_final: 0.8697 (tpt) REVERT: A 696 MET cc_start: 0.8322 (tpt) cc_final: 0.7890 (mmt) REVERT: B 147 PHE cc_start: 0.8700 (m-80) cc_final: 0.8291 (m-10) REVERT: B 292 TYR cc_start: 0.8951 (m-80) cc_final: 0.8665 (m-80) REVERT: B 452 MET cc_start: 0.7381 (pmm) cc_final: 0.7085 (pmm) REVERT: B 563 MET cc_start: 0.7506 (mmt) cc_final: 0.7219 (mmt) REVERT: B 569 MET cc_start: 0.8714 (pmm) cc_final: 0.7622 (pmm) REVERT: B 686 MET cc_start: 0.6909 (mmp) cc_final: 0.6579 (mmp) REVERT: B 906 MET cc_start: 0.8562 (mmp) cc_final: 0.8247 (pmm) REVERT: B 943 MET cc_start: 0.8615 (mmm) cc_final: 0.7445 (mmm) REVERT: C 169 LEU cc_start: 0.9486 (mt) cc_final: 0.9227 (mt) REVERT: C 563 MET cc_start: 0.8439 (tpt) cc_final: 0.7953 (tpt) REVERT: C 635 TYR cc_start: 0.9109 (m-10) cc_final: 0.8900 (m-10) REVERT: C 695 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.8878 (p) REVERT: C 696 MET cc_start: 0.8225 (tpt) cc_final: 0.7935 (tpt) REVERT: C 757 MET cc_start: 0.8512 (tpt) cc_final: 0.8150 (tpp) outliers start: 21 outliers final: 4 residues processed: 144 average time/residue: 0.1875 time to fit residues: 44.6025 Evaluate side-chains 91 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 overall best weight: 14.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 167 HIS A 233 ASN A 280 GLN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 471 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN C 522 GLN C 637 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.027240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.020356 restraints weight = 560661.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.020510 restraints weight = 384013.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.020800 restraints weight = 289768.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.021029 restraints weight = 240540.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.021144 restraints weight = 212485.685| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 28632 Z= 0.355 Angle : 0.861 23.220 39087 Z= 0.438 Chirality : 0.046 0.476 4527 Planarity : 0.006 0.202 4944 Dihedral : 5.550 23.915 3786 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.04 % Rotamer: Outliers : 0.23 % Allowed : 6.11 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3462 helix: 0.79 (0.20), residues: 689 sheet: -0.86 (0.19), residues: 713 loop : -1.32 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 841 TYR 0.026 0.003 TYR C 438 PHE 0.023 0.003 PHE B1172 TRP 0.018 0.002 TRP A 44 HIS 0.008 0.002 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.35 (28521) covalent geometry : angle 0.82892 / 0.43 (38802) SS BOND : bond 0.00552 / 0.40 ( 48) SS BOND : angle 1.66601 / 1.10 ( 96) hydrogen bonds : bond 0.05130 / 3.41 ( 1021) hydrogen bonds : angle 6.47539 / 4.52 ( 2712) link_ALPHA1-3 : bond 0.00740 / 0.32 ( 3) link_ALPHA1-3 : angle 3.50194 / 1.95 ( 9) link_ALPHA1-6 : bond 0.00582 / 0.29 ( 3) link_ALPHA1-6 : angle 2.43761 / 1.34 ( 9) link_BETA1-4 : bond 0.00676 / 0.53 ( 18) link_BETA1-4 : angle 2.32995 / 1.38 ( 54) link_BETA1-6 : bond 0.00752 / 0.30 ( 6) link_BETA1-6 : angle 2.24683 / 1.18 ( 18) link_NAG-ASN : bond 0.00772 / 0.47 ( 33) link_NAG-ASN : angle 3.88855 / 2.28 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8339 (mmt) cc_final: 0.8097 (mmm) REVERT: A 296 ILE cc_start: 0.9437 (mp) cc_final: 0.8963 (mp) REVERT: A 686 MET cc_start: 0.8453 (mmp) cc_final: 0.8214 (mmm) REVERT: A 939 MET cc_start: 0.9450 (tpp) cc_final: 0.9172 (tpp) REVERT: B 147 PHE cc_start: 0.9490 (m-80) cc_final: 0.9104 (m-10) REVERT: B 292 TYR cc_start: 0.9684 (m-80) cc_final: 0.9368 (m-80) REVERT: B 696 MET cc_start: 0.9024 (mmp) cc_final: 0.8521 (mmp) REVERT: B 757 MET cc_start: 0.8900 (mtt) cc_final: 0.8240 (mmp) REVERT: B 906 MET cc_start: 0.9488 (mmp) cc_final: 0.8699 (pmm) REVERT: B 913 MET cc_start: 0.9429 (mtm) cc_final: 0.9100 (mtp) REVERT: B 939 MET cc_start: 0.8851 (ptm) cc_final: 0.8436 (ptp) REVERT: B 943 MET cc_start: 0.9482 (mmm) cc_final: 0.9258 (tpt) REVERT: B 1008 MET cc_start: 0.9310 (ppp) cc_final: 0.9087 (tmm) REVERT: C 84 MET cc_start: 0.9349 (tpt) cc_final: 0.9014 (mmm) REVERT: C 696 MET cc_start: 0.7901 (tpt) cc_final: 0.7575 (tpt) REVERT: C 757 MET cc_start: 0.9485 (tpt) cc_final: 0.8884 (tpp) REVERT: C 1137 MET cc_start: 0.8883 (mpp) cc_final: 0.8578 (mpp) outliers start: 7 outliers final: 3 residues processed: 95 average time/residue: 0.1730 time to fit residues: 28.1313 Evaluate side-chains 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 134 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 36 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 ASN A 466 GLN A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 114 ASN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 HIS C 220 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 522 GLN C 708 GLN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.027748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.020818 restraints weight = 547588.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.021023 restraints weight = 364141.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.021318 restraints weight = 269661.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.021552 restraints weight = 222277.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.021657 restraints weight = 193701.554| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28632 Z= 0.190 Angle : 0.673 21.946 39087 Z= 0.337 Chirality : 0.044 0.464 4527 Planarity : 0.006 0.256 4944 Dihedral : 5.247 29.658 3786 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3462 helix: 1.17 (0.20), residues: 684 sheet: -0.78 (0.19), residues: 687 loop : -1.26 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 841 TYR 0.021 0.002 TYR C 105 PHE 0.038 0.002 PHE A 972 TRP 0.009 0.001 TRP C 310 HIS 0.007 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.19 (28521) covalent geometry : angle 0.63678 / 0.33 (38802) SS BOND : bond 0.00467 / 0.36 ( 48) SS BOND : angle 1.60775 / 0.97 ( 96) hydrogen bonds : bond 0.03935 / 2.57 ( 1021) hydrogen bonds : angle 6.07192 / 4.25 ( 2712) link_ALPHA1-3 : bond 0.00336 / 0.14 ( 3) link_ALPHA1-3 : angle 2.37049 / 1.37 ( 9) link_ALPHA1-6 : bond 0.00297 / 0.15 ( 3) link_ALPHA1-6 : angle 1.79667 / 0.98 ( 9) link_BETA1-4 : bond 0.00690 / 0.54 ( 18) link_BETA1-4 : angle 2.03424 / 1.20 ( 54) link_BETA1-6 : bond 0.00774 / 0.40 ( 6) link_BETA1-6 : angle 2.15216 / 1.15 ( 18) link_NAG-ASN : bond 0.00562 / 0.31 ( 33) link_NAG-ASN : angle 3.68432 / 2.17 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8324 (mmt) cc_final: 0.8069 (mmm) REVERT: A 278 MET cc_start: 0.9432 (tpt) cc_final: 0.9118 (tpp) REVERT: A 296 ILE cc_start: 0.9396 (mp) cc_final: 0.8925 (mp) REVERT: A 686 MET cc_start: 0.8156 (mmp) cc_final: 0.7917 (mmm) REVERT: A 757 MET cc_start: 0.7864 (tpp) cc_final: 0.7519 (tpp) REVERT: A 939 MET cc_start: 0.9465 (tpp) cc_final: 0.9176 (tpp) REVERT: B 147 PHE cc_start: 0.9463 (m-80) cc_final: 0.9187 (m-10) REVERT: B 292 TYR cc_start: 0.9692 (m-80) cc_final: 0.9380 (m-80) REVERT: B 696 MET cc_start: 0.9026 (mmp) cc_final: 0.8568 (mmp) REVERT: B 757 MET cc_start: 0.8880 (mtt) cc_final: 0.8414 (tpp) REVERT: B 906 MET cc_start: 0.9478 (mmp) cc_final: 0.8779 (pmm) REVERT: B 913 MET cc_start: 0.9492 (mtm) cc_final: 0.9179 (mtp) REVERT: B 939 MET cc_start: 0.8779 (ptm) cc_final: 0.8149 (ptp) REVERT: B 943 MET cc_start: 0.9368 (mmm) cc_final: 0.8631 (mmm) REVERT: B 1008 MET cc_start: 0.9269 (ppp) cc_final: 0.8994 (tmm) REVERT: C 84 MET cc_start: 0.9580 (tpt) cc_final: 0.9199 (tpt) REVERT: C 220 ASN cc_start: 0.9643 (OUTLIER) cc_final: 0.9388 (t0) REVERT: C 278 MET cc_start: 0.8023 (mmp) cc_final: 0.7596 (mmp) REVERT: C 696 MET cc_start: 0.7902 (tpt) cc_final: 0.7679 (tpt) REVERT: C 757 MET cc_start: 0.9499 (tpt) cc_final: 0.8878 (tpp) REVERT: C 1137 MET cc_start: 0.9044 (mpp) cc_final: 0.8822 (mpp) outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.1830 time to fit residues: 26.1918 Evaluate side-chains 73 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 260 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 311 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 264 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN C 842 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.027605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.020720 restraints weight = 548467.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.020883 restraints weight = 362387.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.021177 restraints weight = 268496.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.021405 restraints weight = 222141.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.021516 restraints weight = 193823.673| |-----------------------------------------------------------------------------| r_work (final): 0.2438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 28632 Z= 0.177 Angle : 0.660 21.828 39087 Z= 0.326 Chirality : 0.044 0.433 4527 Planarity : 0.005 0.208 4944 Dihedral : 5.088 25.454 3786 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3462 helix: 1.20 (0.20), residues: 689 sheet: -0.89 (0.19), residues: 718 loop : -1.18 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 841 TYR 0.022 0.002 TYR C 241 PHE 0.028 0.002 PHE B 164 TRP 0.008 0.001 TRP B 310 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (28521) covalent geometry : angle 0.62126 / 0.32 (38802) SS BOND : bond 0.00478 / 0.30 ( 48) SS BOND : angle 1.42820 / 0.87 ( 96) hydrogen bonds : bond 0.03696 / 2.41 ( 1021) hydrogen bonds : angle 5.96215 / 4.17 ( 2712) link_ALPHA1-3 : bond 0.00243 / 0.11 ( 3) link_ALPHA1-3 : angle 2.40694 / 1.39 ( 9) link_ALPHA1-6 : bond 0.00251 / 0.12 ( 3) link_ALPHA1-6 : angle 1.74960 / 0.96 ( 9) link_BETA1-4 : bond 0.00726 / 0.57 ( 18) link_BETA1-4 : angle 2.11918 / 1.24 ( 54) link_BETA1-6 : bond 0.00660 / 0.34 ( 6) link_BETA1-6 : angle 2.08034 / 1.15 ( 18) link_NAG-ASN : bond 0.00653 / 0.35 ( 33) link_NAG-ASN : angle 3.84131 / 2.33 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8363 (mmt) cc_final: 0.8131 (mmm) REVERT: A 278 MET cc_start: 0.9437 (tpt) cc_final: 0.9124 (tpp) REVERT: A 296 ILE cc_start: 0.9431 (mp) cc_final: 0.8958 (mp) REVERT: A 686 MET cc_start: 0.8225 (mmp) cc_final: 0.7984 (mmm) REVERT: A 757 MET cc_start: 0.7947 (tpp) cc_final: 0.7707 (tpp) REVERT: A 939 MET cc_start: 0.9526 (tpp) cc_final: 0.9273 (tpp) REVERT: B 148 MET cc_start: 0.9542 (ppp) cc_final: 0.9280 (ppp) REVERT: B 278 MET cc_start: 0.8700 (tpt) cc_final: 0.8013 (tpp) REVERT: B 292 TYR cc_start: 0.9665 (m-80) cc_final: 0.9362 (m-80) REVERT: B 696 MET cc_start: 0.9044 (mmp) cc_final: 0.8589 (mmp) REVERT: B 757 MET cc_start: 0.8969 (mtt) cc_final: 0.8202 (mmm) REVERT: B 906 MET cc_start: 0.9518 (mmp) cc_final: 0.8778 (pmm) REVERT: B 913 MET cc_start: 0.9491 (mtm) cc_final: 0.9172 (mtp) REVERT: B 939 MET cc_start: 0.8777 (ptm) cc_final: 0.8254 (ptp) REVERT: B 943 MET cc_start: 0.9346 (mmm) cc_final: 0.8700 (mmm) REVERT: B 1008 MET cc_start: 0.9337 (ppp) cc_final: 0.9022 (tmm) REVERT: C 84 MET cc_start: 0.9649 (tpt) cc_final: 0.9431 (tpt) REVERT: C 278 MET cc_start: 0.7970 (mmp) cc_final: 0.7524 (mmp) REVERT: C 757 MET cc_start: 0.9533 (tpt) cc_final: 0.8906 (tpp) REVERT: C 943 MET cc_start: 0.9349 (tpt) cc_final: 0.9085 (tpt) REVERT: C 1137 MET cc_start: 0.9076 (mpp) cc_final: 0.8832 (mpp) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1878 time to fit residues: 26.8473 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 227 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 91 optimal weight: 40.0000 chunk 252 optimal weight: 0.6980 chunk 224 optimal weight: 30.0000 chunk 345 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1009 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.028016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.021129 restraints weight = 541333.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.021311 restraints weight = 353957.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021597 restraints weight = 259622.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.021787 restraints weight = 214917.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.021988 restraints weight = 189555.456| |-----------------------------------------------------------------------------| r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28632 Z= 0.130 Angle : 0.624 21.435 39087 Z= 0.306 Chirality : 0.043 0.426 4527 Planarity : 0.005 0.191 4944 Dihedral : 4.892 22.775 3786 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3462 helix: 1.32 (0.20), residues: 690 sheet: -0.78 (0.19), residues: 710 loop : -1.11 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 841 TYR 0.016 0.001 TYR A 689 PHE 0.020 0.001 PHE A 972 TRP 0.007 0.001 TRP C 310 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (28521) covalent geometry : angle 0.58549 / 0.30 (38802) SS BOND : bond 0.00314 / 0.24 ( 48) SS BOND : angle 1.38729 / 0.87 ( 96) hydrogen bonds : bond 0.03408 / 2.22 ( 1021) hydrogen bonds : angle 5.72707 / 4.00 ( 2712) link_ALPHA1-3 : bond 0.00251 / 0.12 ( 3) link_ALPHA1-3 : angle 2.07981 / 1.20 ( 9) link_ALPHA1-6 : bond 0.00271 / 0.13 ( 3) link_ALPHA1-6 : angle 1.62024 / 0.88 ( 9) link_BETA1-4 : bond 0.00680 / 0.52 ( 18) link_BETA1-4 : angle 1.97309 / 1.19 ( 54) link_BETA1-6 : bond 0.00702 / 0.38 ( 6) link_BETA1-6 : angle 1.98076 / 1.13 ( 18) link_NAG-ASN : bond 0.00703 / 0.35 ( 33) link_NAG-ASN : angle 3.72267 / 2.28 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8344 (mmt) cc_final: 0.8121 (mmm) REVERT: A 278 MET cc_start: 0.9458 (tpt) cc_final: 0.9216 (tpp) REVERT: A 296 ILE cc_start: 0.9398 (mp) cc_final: 0.8956 (mp) REVERT: A 686 MET cc_start: 0.8251 (mmp) cc_final: 0.8009 (mmm) REVERT: A 696 MET cc_start: 0.8239 (mmt) cc_final: 0.7825 (mmm) REVERT: A 939 MET cc_start: 0.9529 (tpp) cc_final: 0.9258 (tpp) REVERT: B 278 MET cc_start: 0.8646 (tpt) cc_final: 0.8159 (tpp) REVERT: B 292 TYR cc_start: 0.9655 (m-80) cc_final: 0.9340 (m-80) REVERT: B 696 MET cc_start: 0.9024 (mmp) cc_final: 0.8566 (mmp) REVERT: B 757 MET cc_start: 0.9060 (mtt) cc_final: 0.8473 (mmp) REVERT: B 906 MET cc_start: 0.9513 (mmp) cc_final: 0.8704 (pmm) REVERT: B 913 MET cc_start: 0.9472 (mtm) cc_final: 0.9130 (mtp) REVERT: B 939 MET cc_start: 0.8927 (ptm) cc_final: 0.8201 (ptp) REVERT: B 943 MET cc_start: 0.9325 (mmm) cc_final: 0.8332 (mmm) REVERT: B 1008 MET cc_start: 0.9332 (ppp) cc_final: 0.9053 (tmm) REVERT: C 278 MET cc_start: 0.8015 (mmp) cc_final: 0.7602 (mmp) REVERT: C 757 MET cc_start: 0.9549 (tpt) cc_final: 0.8924 (tpp) REVERT: C 943 MET cc_start: 0.9410 (tpt) cc_final: 0.9181 (tpt) REVERT: C 1137 MET cc_start: 0.9116 (mpp) cc_final: 0.8843 (mpp) outliers start: 3 outliers final: 1 residues processed: 82 average time/residue: 0.1782 time to fit residues: 25.2191 Evaluate side-chains 69 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 213 optimal weight: 30.0000 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 322 optimal weight: 20.0000 chunk 176 optimal weight: 30.0000 chunk 290 optimal weight: 6.9990 chunk 308 optimal weight: 2.9990 chunk 127 optimal weight: 40.0000 chunk 247 optimal weight: 0.8980 chunk 210 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.027414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.020514 restraints weight = 548511.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.020669 restraints weight = 363692.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.020969 restraints weight = 269360.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.021195 restraints weight = 220251.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.021327 restraints weight = 194982.171| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28632 Z= 0.170 Angle : 0.649 21.649 39087 Z= 0.320 Chirality : 0.043 0.402 4527 Planarity : 0.005 0.157 4944 Dihedral : 4.960 31.224 3786 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.74 (0.14), residues: 3462 helix: 1.48 (0.20), residues: 694 sheet: -0.77 (0.19), residues: 697 loop : -1.10 (0.14), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 841 TYR 0.018 0.002 TYR B 609 PHE 0.022 0.002 PHE B 164 TRP 0.010 0.001 TRP B 310 HIS 0.004 0.001 HIS A1138 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (28521) covalent geometry : angle 0.61038 / 0.31 (38802) SS BOND : bond 0.00366 / 0.28 ( 48) SS BOND : angle 1.43773 / 0.89 ( 96) hydrogen bonds : bond 0.03552 / 2.32 ( 1021) hydrogen bonds : angle 5.80560 / 4.04 ( 2712) link_ALPHA1-3 : bond 0.00237 / 0.11 ( 3) link_ALPHA1-3 : angle 2.32110 / 1.33 ( 9) link_ALPHA1-6 : bond 0.00249 / 0.13 ( 3) link_ALPHA1-6 : angle 1.70823 / 0.93 ( 9) link_BETA1-4 : bond 0.00731 / 0.59 ( 18) link_BETA1-4 : angle 2.12734 / 1.24 ( 54) link_BETA1-6 : bond 0.00614 / 0.30 ( 6) link_BETA1-6 : angle 1.88423 / 1.06 ( 18) link_NAG-ASN : bond 0.00613 / 0.33 ( 33) link_NAG-ASN : angle 3.79406 / 2.33 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8406 (mmt) cc_final: 0.8187 (mmm) REVERT: A 296 ILE cc_start: 0.9404 (mp) cc_final: 0.9044 (mp) REVERT: A 686 MET cc_start: 0.8272 (mmp) cc_final: 0.8046 (mmm) REVERT: A 696 MET cc_start: 0.8312 (mmt) cc_final: 0.8031 (mmp) REVERT: A 757 MET cc_start: 0.7761 (tpp) cc_final: 0.7467 (tpp) REVERT: A 939 MET cc_start: 0.9574 (tpp) cc_final: 0.9321 (tpp) REVERT: B 147 PHE cc_start: 0.9540 (m-80) cc_final: 0.9207 (m-10) REVERT: B 278 MET cc_start: 0.8695 (tpt) cc_final: 0.7846 (tpp) REVERT: B 292 TYR cc_start: 0.9673 (m-80) cc_final: 0.9363 (m-80) REVERT: B 696 MET cc_start: 0.9004 (mmp) cc_final: 0.8543 (mmp) REVERT: B 757 MET cc_start: 0.9035 (mtt) cc_final: 0.8450 (mmp) REVERT: B 906 MET cc_start: 0.9533 (mmp) cc_final: 0.8788 (pmm) REVERT: B 913 MET cc_start: 0.9501 (mtm) cc_final: 0.9236 (mtp) REVERT: B 939 MET cc_start: 0.8940 (ptm) cc_final: 0.8404 (ptp) REVERT: B 943 MET cc_start: 0.9314 (mmm) cc_final: 0.8450 (mmm) REVERT: C 278 MET cc_start: 0.7830 (mmp) cc_final: 0.7446 (mmp) REVERT: C 757 MET cc_start: 0.9530 (tpt) cc_final: 0.8931 (tpp) REVERT: C 943 MET cc_start: 0.9360 (tpt) cc_final: 0.9114 (tpt) REVERT: C 1137 MET cc_start: 0.9128 (mpp) cc_final: 0.8849 (mpp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1658 time to fit residues: 23.1372 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 345 optimal weight: 9.9990 chunk 256 optimal weight: 20.0000 chunk 171 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 303 optimal weight: 40.0000 chunk 118 optimal weight: 20.0000 chunk 309 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.026726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.019843 restraints weight = 557191.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.019991 restraints weight = 372007.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020275 restraints weight = 277565.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.020502 restraints weight = 225775.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.020610 restraints weight = 199436.048| |-----------------------------------------------------------------------------| r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28632 Z= 0.202 Angle : 0.686 21.689 39087 Z= 0.339 Chirality : 0.044 0.385 4527 Planarity : 0.005 0.116 4944 Dihedral : 5.117 26.539 3786 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 19.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3462 helix: 1.30 (0.20), residues: 706 sheet: -0.78 (0.19), residues: 659 loop : -1.12 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 841 TYR 0.023 0.002 TYR B 609 PHE 0.032 0.002 PHE B 164 TRP 0.010 0.001 TRP B 310 HIS 0.007 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.20 (28521) covalent geometry : angle 0.64525 / 0.33 (38802) SS BOND : bond 0.00445 / 0.31 ( 48) SS BOND : angle 1.65813 / 1.03 ( 96) hydrogen bonds : bond 0.03688 / 2.43 ( 1021) hydrogen bonds : angle 5.97961 / 4.16 ( 2712) link_ALPHA1-3 : bond 0.00302 / 0.14 ( 3) link_ALPHA1-3 : angle 2.47606 / 1.42 ( 9) link_ALPHA1-6 : bond 0.00233 / 0.12 ( 3) link_ALPHA1-6 : angle 1.87057 / 1.02 ( 9) link_BETA1-4 : bond 0.00703 / 0.46 ( 18) link_BETA1-4 : angle 2.01330 / 1.17 ( 54) link_BETA1-6 : bond 0.00663 / 0.36 ( 6) link_BETA1-6 : angle 1.94914 / 1.10 ( 18) link_NAG-ASN : bond 0.00842 / 0.45 ( 33) link_NAG-ASN : angle 4.01693 / 2.56 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8447 (mmt) cc_final: 0.8219 (mmm) REVERT: A 278 MET cc_start: 0.9327 (tpt) cc_final: 0.9020 (tpp) REVERT: A 296 ILE cc_start: 0.9388 (mp) cc_final: 0.9067 (mp) REVERT: A 696 MET cc_start: 0.8371 (mmt) cc_final: 0.8116 (mmp) REVERT: A 939 MET cc_start: 0.9556 (tpp) cc_final: 0.9306 (tpp) REVERT: B 147 PHE cc_start: 0.9483 (m-80) cc_final: 0.9265 (m-10) REVERT: B 148 MET cc_start: 0.9698 (tmm) cc_final: 0.9443 (ppp) REVERT: B 278 MET cc_start: 0.8510 (tpt) cc_final: 0.7681 (tpp) REVERT: B 292 TYR cc_start: 0.9682 (m-80) cc_final: 0.9400 (m-80) REVERT: B 696 MET cc_start: 0.9001 (mmp) cc_final: 0.8542 (mmp) REVERT: B 757 MET cc_start: 0.9087 (mtt) cc_final: 0.8565 (mmp) REVERT: B 906 MET cc_start: 0.9515 (mmp) cc_final: 0.8777 (pmm) REVERT: B 913 MET cc_start: 0.9500 (mtm) cc_final: 0.9145 (mtp) REVERT: B 939 MET cc_start: 0.8959 (ptm) cc_final: 0.8442 (ptp) REVERT: B 943 MET cc_start: 0.9321 (mmm) cc_final: 0.8425 (mmm) REVERT: C 278 MET cc_start: 0.7891 (mmp) cc_final: 0.7542 (mmp) REVERT: C 757 MET cc_start: 0.9502 (tpt) cc_final: 0.8919 (tpp) REVERT: C 1137 MET cc_start: 0.9177 (mpp) cc_final: 0.8885 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1803 time to fit residues: 23.7874 Evaluate side-chains 66 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 4 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 342 optimal weight: 2.9990 chunk 316 optimal weight: 0.6980 chunk 226 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 13 optimal weight: 50.0000 chunk 219 optimal weight: 10.0000 chunk 327 optimal weight: 30.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.027540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.020670 restraints weight = 546162.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.020821 restraints weight = 356345.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021131 restraints weight = 261454.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.021377 restraints weight = 213054.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.021505 restraints weight = 187791.132| |-----------------------------------------------------------------------------| r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28632 Z= 0.125 Angle : 0.635 21.233 39087 Z= 0.309 Chirality : 0.044 0.396 4527 Planarity : 0.004 0.072 4944 Dihedral : 4.905 25.968 3786 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.03 % Allowed : 1.13 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.14), residues: 3462 helix: 1.54 (0.20), residues: 697 sheet: -0.65 (0.19), residues: 663 loop : -1.08 (0.14), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 841 TYR 0.036 0.001 TYR C 314 PHE 0.021 0.001 PHE B 164 TRP 0.007 0.001 TRP C 44 HIS 0.004 0.001 HIS B 81 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (28521) covalent geometry : angle 0.59589 / 0.30 (38802) SS BOND : bond 0.00330 / 0.25 ( 48) SS BOND : angle 1.53220 / 0.97 ( 96) hydrogen bonds : bond 0.03297 / 2.15 ( 1021) hydrogen bonds : angle 5.70468 / 3.97 ( 2712) link_ALPHA1-3 : bond 0.00256 / 0.12 ( 3) link_ALPHA1-3 : angle 2.04888 / 1.17 ( 9) link_ALPHA1-6 : bond 0.00275 / 0.12 ( 3) link_ALPHA1-6 : angle 1.59093 / 0.85 ( 9) link_BETA1-4 : bond 0.00719 / 0.55 ( 18) link_BETA1-4 : angle 1.92127 / 1.14 ( 54) link_BETA1-6 : bond 0.00696 / 0.37 ( 6) link_BETA1-6 : angle 1.88148 / 1.09 ( 18) link_NAG-ASN : bond 0.00684 / 0.35 ( 33) link_NAG-ASN : angle 3.77938 / 2.37 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8401 (mmt) cc_final: 0.8181 (mmm) REVERT: A 278 MET cc_start: 0.9338 (tpt) cc_final: 0.8989 (tpp) REVERT: A 296 ILE cc_start: 0.9354 (mp) cc_final: 0.9037 (mp) REVERT: A 696 MET cc_start: 0.8384 (mmt) cc_final: 0.8142 (mmp) REVERT: A 939 MET cc_start: 0.9562 (tpp) cc_final: 0.9294 (tpp) REVERT: B 84 MET cc_start: 0.9062 (tpt) cc_final: 0.8820 (mmm) REVERT: B 147 PHE cc_start: 0.9487 (m-80) cc_final: 0.9246 (m-10) REVERT: B 148 MET cc_start: 0.9694 (tmm) cc_final: 0.9410 (ppp) REVERT: B 278 MET cc_start: 0.8395 (tpt) cc_final: 0.7614 (tpp) REVERT: B 292 TYR cc_start: 0.9680 (m-80) cc_final: 0.9385 (m-80) REVERT: B 696 MET cc_start: 0.8998 (mmp) cc_final: 0.8533 (mmp) REVERT: B 757 MET cc_start: 0.9063 (mtt) cc_final: 0.8543 (mmp) REVERT: B 906 MET cc_start: 0.9522 (mmp) cc_final: 0.8761 (pmm) REVERT: B 913 MET cc_start: 0.9465 (mtm) cc_final: 0.9102 (mtp) REVERT: B 943 MET cc_start: 0.9247 (mmm) cc_final: 0.8378 (tpt) REVERT: C 161 MET cc_start: 0.8738 (mmp) cc_final: 0.8437 (mmp) REVERT: C 278 MET cc_start: 0.7829 (mmp) cc_final: 0.7481 (mmp) REVERT: C 757 MET cc_start: 0.9491 (tpt) cc_final: 0.8912 (tpp) REVERT: C 1137 MET cc_start: 0.9249 (mpp) cc_final: 0.8959 (mpp) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.1630 time to fit residues: 22.7379 Evaluate side-chains 66 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 164 optimal weight: 30.0000 chunk 100 optimal weight: 6.9990 chunk 57 optimal weight: 40.0000 chunk 161 optimal weight: 40.0000 chunk 126 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 96 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN B 348 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.026050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.019203 restraints weight = 571954.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.019313 restraints weight = 385930.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.019596 restraints weight = 290080.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.019808 restraints weight = 239063.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.019922 restraints weight = 210608.531| |-----------------------------------------------------------------------------| r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28632 Z= 0.266 Angle : 0.751 21.980 39087 Z= 0.374 Chirality : 0.045 0.366 4527 Planarity : 0.005 0.059 4944 Dihedral : 5.284 25.022 3786 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3462 helix: 1.21 (0.20), residues: 702 sheet: -1.06 (0.19), residues: 679 loop : -1.19 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 235 TYR 0.022 0.002 TYR B1171 PHE 0.035 0.002 PHE B 164 TRP 0.014 0.002 TRP B 310 HIS 0.007 0.002 HIS B1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.27 (28521) covalent geometry : angle 0.71447 / 0.37 (38802) SS BOND : bond 0.00650 / 0.51 ( 48) SS BOND : angle 1.68191 / 1.08 ( 96) hydrogen bonds : bond 0.04125 / 2.73 ( 1021) hydrogen bonds : angle 6.20844 / 4.31 ( 2712) link_ALPHA1-3 : bond 0.00525 / 0.23 ( 3) link_ALPHA1-3 : angle 2.83550 / 1.62 ( 9) link_ALPHA1-6 : bond 0.00322 / 0.16 ( 3) link_ALPHA1-6 : angle 2.09767 / 1.14 ( 9) link_BETA1-4 : bond 0.00484 / 0.41 ( 18) link_BETA1-4 : angle 2.06469 / 1.20 ( 54) link_BETA1-6 : bond 0.00623 / 0.32 ( 6) link_BETA1-6 : angle 1.97871 / 1.08 ( 18) link_NAG-ASN : bond 0.00767 / 0.45 ( 33) link_NAG-ASN : angle 3.93187 / 2.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8379 (mmt) cc_final: 0.8165 (mmm) REVERT: A 278 MET cc_start: 0.9318 (tpt) cc_final: 0.9018 (tpp) REVERT: A 296 ILE cc_start: 0.9380 (mp) cc_final: 0.9117 (mp) REVERT: A 696 MET cc_start: 0.8531 (mmt) cc_final: 0.8293 (mmp) REVERT: A 939 MET cc_start: 0.9595 (tpp) cc_final: 0.9365 (tpp) REVERT: B 147 PHE cc_start: 0.9477 (m-80) cc_final: 0.9055 (m-10) REVERT: B 278 MET cc_start: 0.8411 (tpt) cc_final: 0.7622 (tpp) REVERT: B 696 MET cc_start: 0.9004 (mmp) cc_final: 0.8556 (mmp) REVERT: B 757 MET cc_start: 0.9087 (mtt) cc_final: 0.8687 (mtt) REVERT: B 913 MET cc_start: 0.9512 (mtm) cc_final: 0.9147 (mtp) REVERT: B 943 MET cc_start: 0.9308 (mmm) cc_final: 0.8598 (tpp) REVERT: C 148 MET cc_start: 0.9777 (ppp) cc_final: 0.9576 (ppp) REVERT: C 161 MET cc_start: 0.8638 (mmp) cc_final: 0.8433 (mmp) REVERT: C 278 MET cc_start: 0.7997 (mmp) cc_final: 0.7697 (mmp) REVERT: C 757 MET cc_start: 0.9487 (tpt) cc_final: 0.8989 (tpp) REVERT: C 1137 MET cc_start: 0.9215 (mpp) cc_final: 0.8956 (mpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1666 time to fit residues: 22.0633 Evaluate side-chains 66 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 180 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 319 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 270 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 183 optimal weight: 6.9990 chunk 165 optimal weight: 0.0770 chunk 14 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.026819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.019963 restraints weight = 554329.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.020140 restraints weight = 363940.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.020426 restraints weight = 267884.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.020661 restraints weight = 223658.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.020779 restraints weight = 194627.893| |-----------------------------------------------------------------------------| r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28632 Z= 0.152 Angle : 0.661 21.341 39087 Z= 0.323 Chirality : 0.044 0.378 4527 Planarity : 0.004 0.053 4944 Dihedral : 5.103 24.572 3786 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.03 % Allowed : 0.50 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.14), residues: 3462 helix: 1.34 (0.20), residues: 717 sheet: -0.77 (0.19), residues: 648 loop : -1.17 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 181 TYR 0.015 0.002 TYR B 641 PHE 0.025 0.001 PHE B 164 TRP 0.013 0.001 TRP C 44 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (28521) covalent geometry : angle 0.62155 / 0.31 (38802) SS BOND : bond 0.00355 / 0.27 ( 48) SS BOND : angle 1.46088 / 0.93 ( 96) hydrogen bonds : bond 0.03448 / 2.26 ( 1021) hydrogen bonds : angle 5.88062 / 4.09 ( 2712) link_ALPHA1-3 : bond 0.00276 / 0.13 ( 3) link_ALPHA1-3 : angle 2.20359 / 1.27 ( 9) link_ALPHA1-6 : bond 0.00179 / 0.09 ( 3) link_ALPHA1-6 : angle 1.65602 / 0.89 ( 9) link_BETA1-4 : bond 0.00638 / 0.49 ( 18) link_BETA1-4 : angle 1.86288 / 1.09 ( 54) link_BETA1-6 : bond 0.00682 / 0.37 ( 6) link_BETA1-6 : angle 1.94316 / 1.12 ( 18) link_NAG-ASN : bond 0.00661 / 0.35 ( 33) link_NAG-ASN : angle 3.95343 / 2.47 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8398 (mmt) cc_final: 0.8176 (mmm) REVERT: A 278 MET cc_start: 0.9366 (tpt) cc_final: 0.9054 (tpp) REVERT: A 296 ILE cc_start: 0.9353 (mp) cc_final: 0.9131 (mp) REVERT: A 939 MET cc_start: 0.9578 (tpp) cc_final: 0.9338 (tpp) REVERT: B 147 PHE cc_start: 0.9446 (m-80) cc_final: 0.9171 (m-10) REVERT: B 278 MET cc_start: 0.8281 (tpt) cc_final: 0.7519 (tpp) REVERT: B 292 TYR cc_start: 0.9678 (m-80) cc_final: 0.9395 (m-80) REVERT: B 696 MET cc_start: 0.9028 (mmp) cc_final: 0.8583 (mmp) REVERT: B 757 MET cc_start: 0.9057 (mtt) cc_final: 0.8753 (mmm) REVERT: B 906 MET cc_start: 0.9460 (mmp) cc_final: 0.8694 (pmm) REVERT: B 913 MET cc_start: 0.9510 (mtm) cc_final: 0.9171 (mtp) REVERT: B 943 MET cc_start: 0.9280 (mmm) cc_final: 0.8843 (tpp) REVERT: C 161 MET cc_start: 0.8607 (mmp) cc_final: 0.8380 (mmp) REVERT: C 278 MET cc_start: 0.7970 (mmp) cc_final: 0.7671 (mmp) REVERT: C 757 MET cc_start: 0.9452 (tpt) cc_final: 0.8927 (tpp) REVERT: C 1137 MET cc_start: 0.9287 (mpp) cc_final: 0.8993 (mpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1728 time to fit residues: 22.5062 Evaluate side-chains 65 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 152 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 275 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 chunk 195 optimal weight: 9.9990 chunk 347 optimal weight: 30.0000 chunk 53 optimal weight: 50.0000 chunk 260 optimal weight: 20.0000 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.025930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2489 r_free = 0.2489 target = 0.019091 restraints weight = 568870.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.019181 restraints weight = 385693.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.019485 restraints weight = 290460.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.019701 restraints weight = 239096.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.019857 restraints weight = 209482.245| |-----------------------------------------------------------------------------| r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 28632 Z= 0.255 Angle : 0.745 21.835 39087 Z= 0.370 Chirality : 0.045 0.367 4527 Planarity : 0.005 0.053 4944 Dihedral : 5.358 23.908 3786 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.14), residues: 3462 helix: 1.18 (0.20), residues: 704 sheet: -1.10 (0.19), residues: 662 loop : -1.25 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 758 TYR 0.021 0.002 TYR B1171 PHE 0.026 0.002 PHE B 164 TRP 0.012 0.002 TRP B 310 HIS 0.006 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.26 (28521) covalent geometry : angle 0.70819 / 0.36 (38802) SS BOND : bond 0.00450 / 0.33 ( 48) SS BOND : angle 1.69157 / 1.07 ( 96) hydrogen bonds : bond 0.04030 / 2.65 ( 1021) hydrogen bonds : angle 6.23488 / 4.34 ( 2712) link_ALPHA1-3 : bond 0.00583 / 0.25 ( 3) link_ALPHA1-3 : angle 2.75470 / 1.59 ( 9) link_ALPHA1-6 : bond 0.00248 / 0.11 ( 3) link_ALPHA1-6 : angle 1.92978 / 1.06 ( 9) link_BETA1-4 : bond 0.00494 / 0.41 ( 18) link_BETA1-4 : angle 1.94760 / 1.14 ( 54) link_BETA1-6 : bond 0.00631 / 0.33 ( 6) link_BETA1-6 : angle 2.03695 / 1.11 ( 18) link_NAG-ASN : bond 0.00732 / 0.43 ( 33) link_NAG-ASN : angle 3.96065 / 2.48 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4008.58 seconds wall clock time: 71 minutes 31.01 seconds (4291.01 seconds total)