Starting phenix.real_space_refine on Mon Aug 25 13:24:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_33948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_33948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_33948.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_33948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymz_33948/08_2025/7ymz_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.61, per 1000 atoms: 0.20 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: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.05 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: 7.14 Time building geometry restraints manager: 3.31 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 - 25.22: 16719 25.22 - 50.44: 870 50.44 - 75.66: 132 75.66 - 100.88: 65 100.88 - 126.10: 25 Dihedral angle restraints: 17811 sinusoidal: 7620 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 17808 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: 0.03 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: 1.400 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.630 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 16.428 126.102 11157 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 aren 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 covalent geometry : bond 0.00498 (28521) covalent geometry : angle 0.89156 (38802) SS BOND : bond 0.00209 ( 48) SS BOND : angle 1.45948 ( 96) hydrogen bonds : bond 0.14178 ( 1021) hydrogen bonds : angle 6.93291 ( 2712) link_ALPHA1-3 : bond 0.00256 ( 3) link_ALPHA1-3 : angle 1.93181 ( 9) link_ALPHA1-6 : bond 0.00311 ( 3) link_ALPHA1-6 : angle 1.66194 ( 9) link_BETA1-4 : bond 0.01096 ( 18) link_BETA1-4 : angle 3.54134 ( 54) link_BETA1-6 : bond 0.01226 ( 6) link_BETA1-6 : angle 2.87567 ( 18) link_NAG-ASN : bond 0.01182 ( 33) link_NAG-ASN : angle 4.69761 ( 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 : 1.009 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: 0.1534 time to fit residues: 36.4858 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 : 0.873 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 280 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B1072 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 GLN C 522 GLN C 637 ASN C 647 ASN C 907 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN C1129 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.026959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.020054 restraints weight = 565773.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.020186 restraints weight = 388744.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.020467 restraints weight = 294629.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.020683 restraints weight = 245219.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.020799 restraints weight = 217502.512| |-----------------------------------------------------------------------------| r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 28632 Z= 0.369 Angle : 0.911 22.905 39087 Z= 0.458 Chirality : 0.047 0.534 4527 Planarity : 0.006 0.201 4944 Dihedral : 10.707 110.989 5067 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 0.27 % Allowed : 6.75 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.14), residues: 3462 helix: 0.75 (0.19), residues: 685 sheet: -0.98 (0.18), residues: 733 loop : -1.31 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 841 TYR 0.028 0.003 TYR C 438 PHE 0.026 0.003 PHE B1172 TRP 0.021 0.003 TRP A 44 HIS 0.009 0.002 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00715 (28521) covalent geometry : angle 0.87438 (38802) SS BOND : bond 0.01628 ( 48) SS BOND : angle 1.81246 ( 96) hydrogen bonds : bond 0.05210 ( 1021) hydrogen bonds : angle 6.56448 ( 2712) link_ALPHA1-3 : bond 0.00777 ( 3) link_ALPHA1-3 : angle 5.62379 ( 9) link_ALPHA1-6 : bond 0.00502 ( 3) link_ALPHA1-6 : angle 2.07113 ( 9) link_BETA1-4 : bond 0.00787 ( 18) link_BETA1-4 : angle 2.69382 ( 54) link_BETA1-6 : bond 0.01106 ( 6) link_BETA1-6 : angle 2.82695 ( 18) link_NAG-ASN : bond 0.00812 ( 33) link_NAG-ASN : angle 4.04000 ( 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 96 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.749 Fit side-chains 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: 0.8095 (mmm) REVERT: A 278 MET cc_start: 0.9079 (tpp) cc_final: 0.8863 (tpp) REVERT: A 296 ILE cc_start: 0.9440 (mp) cc_final: 0.8959 (mp) REVERT: A 686 MET cc_start: 0.8401 (mmp) cc_final: 0.8184 (mmm) REVERT: A 939 MET cc_start: 0.9453 (tpp) cc_final: 0.9176 (tpp) REVERT: A 943 MET cc_start: 0.9251 (mmm) cc_final: 0.8935 (mmm) REVERT: B 147 PHE cc_start: 0.9492 (m-80) cc_final: 0.9125 (m-10) REVERT: B 292 TYR cc_start: 0.9682 (m-80) cc_final: 0.9366 (m-80) REVERT: B 696 MET cc_start: 0.9024 (mmp) cc_final: 0.8395 (mmp) REVERT: B 757 MET cc_start: 0.9025 (mtt) cc_final: 0.8554 (mmm) REVERT: B 906 MET cc_start: 0.9493 (mmp) cc_final: 0.8717 (pmm) REVERT: B 913 MET cc_start: 0.9496 (mtm) cc_final: 0.9244 (mtp) REVERT: B 939 MET cc_start: 0.8969 (ptm) cc_final: 0.8408 (ptm) REVERT: B 943 MET cc_start: 0.9466 (mmm) cc_final: 0.8894 (mmm) REVERT: B 1008 MET cc_start: 0.9326 (ppp) cc_final: 0.9084 (tmm) REVERT: C 84 MET cc_start: 0.9404 (tpt) cc_final: 0.9105 (mmm) REVERT: C 696 MET cc_start: 0.7971 (tpt) cc_final: 0.7645 (tpt) REVERT: C 757 MET cc_start: 0.9502 (tpt) cc_final: 0.8880 (tpp) REVERT: C 1137 MET cc_start: 0.8879 (mpp) cc_final: 0.8582 (mpp) outliers start: 8 outliers final: 2 residues processed: 96 average time/residue: 0.1392 time to fit residues: 22.8699 Evaluate side-chains 71 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 5.9990 chunk 341 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 36 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 192 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 217 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 398 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 395 GLN C 471 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.027810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.020913 restraints weight = 546619.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.021090 restraints weight = 362161.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.021383 restraints weight = 268700.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.021621 restraints weight = 220645.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021735 restraints weight = 192687.489| |-----------------------------------------------------------------------------| r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28632 Z= 0.175 Angle : 0.679 21.627 39087 Z= 0.335 Chirality : 0.045 0.490 4527 Planarity : 0.006 0.252 4944 Dihedral : 9.907 114.120 5067 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % Rotamer: Outliers : 0.10 % Allowed : 3.19 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3462 helix: 1.14 (0.20), residues: 685 sheet: -0.79 (0.19), residues: 687 loop : -1.26 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 841 TYR 0.021 0.002 TYR C 105 PHE 0.038 0.001 PHE A 972 TRP 0.009 0.001 TRP C 310 HIS 0.007 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00363 (28521) covalent geometry : angle 0.63395 (38802) SS BOND : bond 0.00455 ( 48) SS BOND : angle 1.59015 ( 96) hydrogen bonds : bond 0.03864 ( 1021) hydrogen bonds : angle 6.07910 ( 2712) link_ALPHA1-3 : bond 0.00771 ( 3) link_ALPHA1-3 : angle 3.80407 ( 9) link_ALPHA1-6 : bond 0.00532 ( 3) link_ALPHA1-6 : angle 1.61743 ( 9) link_BETA1-4 : bond 0.00644 ( 18) link_BETA1-4 : angle 2.33785 ( 54) link_BETA1-6 : bond 0.01158 ( 6) link_BETA1-6 : angle 2.77392 ( 18) link_NAG-ASN : bond 0.00544 ( 33) link_NAG-ASN : angle 4.01256 ( 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: 3 poor density : 81 time to evaluate : 0.818 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: 0.8363 (mmt) cc_final: 0.8106 (mmm) REVERT: A 278 MET cc_start: 0.9039 (tpp) cc_final: 0.8692 (tpp) REVERT: A 296 ILE cc_start: 0.9376 (mp) cc_final: 0.8901 (mp) REVERT: A 686 MET cc_start: 0.8214 (mmp) cc_final: 0.7995 (mmm) REVERT: A 757 MET cc_start: 0.7829 (tpp) cc_final: 0.7507 (tpp) REVERT: A 906 MET cc_start: 0.8687 (mmm) cc_final: 0.8485 (mmm) REVERT: A 939 MET cc_start: 0.9468 (tpp) cc_final: 0.9179 (tpp) REVERT: A 943 MET cc_start: 0.9262 (mmm) cc_final: 0.8876 (mmm) REVERT: B 147 PHE cc_start: 0.9479 (m-80) cc_final: 0.9206 (m-10) REVERT: B 292 TYR cc_start: 0.9703 (m-80) cc_final: 0.9393 (m-80) REVERT: B 696 MET cc_start: 0.9036 (mmp) cc_final: 0.8598 (mmp) REVERT: B 757 MET cc_start: 0.8976 (mtt) cc_final: 0.8203 (mmm) REVERT: B 906 MET cc_start: 0.9525 (mmp) cc_final: 0.8829 (pmm) REVERT: B 913 MET cc_start: 0.9481 (mtm) cc_final: 0.9173 (mtp) REVERT: B 939 MET cc_start: 0.8828 (ptm) cc_final: 0.8157 (ptp) REVERT: B 943 MET cc_start: 0.9362 (mmm) cc_final: 0.8675 (mmm) REVERT: B 1008 MET cc_start: 0.9288 (ppp) cc_final: 0.8994 (tmm) REVERT: C 84 MET cc_start: 0.9576 (tpt) cc_final: 0.9189 (tpt) REVERT: C 220 ASN cc_start: 0.9639 (OUTLIER) cc_final: 0.9392 (t0) REVERT: C 757 MET cc_start: 0.9500 (tpt) cc_final: 0.8902 (tpp) REVERT: C 1137 MET cc_start: 0.9063 (mpp) cc_final: 0.8847 (mpp) outliers start: 3 outliers final: 0 residues processed: 84 average time/residue: 0.1572 time to fit residues: 22.4819 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 : 1.006 ------------------------------------------------------------------------------- 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: 2.9990 chunk 311 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 264 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 335 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 223 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 324 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 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 226 ASN C 522 GLN C 842 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.028051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.021188 restraints weight = 541558.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.021373 restraints weight = 353773.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.021675 restraints weight = 260279.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.021884 restraints weight = 214016.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.021987 restraints weight = 187746.234| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28632 Z= 0.142 Angle : 0.645 21.569 39087 Z= 0.314 Chirality : 0.044 0.474 4527 Planarity : 0.005 0.196 4944 Dihedral : 9.264 112.591 5067 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.14), residues: 3462 helix: 1.23 (0.20), residues: 695 sheet: -0.61 (0.19), residues: 662 loop : -1.20 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 841 TYR 0.022 0.001 TYR C 241 PHE 0.026 0.001 PHE A 972 TRP 0.007 0.001 TRP C 310 HIS 0.004 0.001 HIS C1146 Details of bonding type rmsd covalent geometry : bond 0.00300 (28521) covalent geometry : angle 0.59888 (38802) SS BOND : bond 0.00326 ( 48) SS BOND : angle 1.38984 ( 96) hydrogen bonds : bond 0.03526 ( 1021) hydrogen bonds : angle 5.83056 ( 2712) link_ALPHA1-3 : bond 0.00858 ( 3) link_ALPHA1-3 : angle 3.68906 ( 9) link_ALPHA1-6 : bond 0.00769 ( 3) link_ALPHA1-6 : angle 1.42227 ( 9) link_BETA1-4 : bond 0.00736 ( 18) link_BETA1-4 : angle 2.45478 ( 54) link_BETA1-6 : bond 0.01110 ( 6) link_BETA1-6 : angle 2.77979 ( 18) link_NAG-ASN : bond 0.00588 ( 33) link_NAG-ASN : angle 3.93496 ( 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 83 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8319 (mmt) cc_final: 0.8094 (mmm) REVERT: A 278 MET cc_start: 0.9012 (tpp) cc_final: 0.8748 (tpp) REVERT: A 296 ILE cc_start: 0.9419 (mp) cc_final: 0.8936 (mp) REVERT: A 686 MET cc_start: 0.8311 (mmp) cc_final: 0.8057 (mmm) REVERT: A 696 MET cc_start: 0.8522 (mmt) cc_final: 0.8056 (mmm) REVERT: A 757 MET cc_start: 0.7878 (tpp) cc_final: 0.7641 (tpp) REVERT: A 939 MET cc_start: 0.9507 (tpp) cc_final: 0.9242 (tpp) REVERT: B 148 MET cc_start: 0.9513 (ppp) cc_final: 0.9249 (ppp) REVERT: B 278 MET cc_start: 0.8703 (tpt) cc_final: 0.8111 (tpp) REVERT: B 292 TYR cc_start: 0.9665 (m-80) cc_final: 0.9363 (m-80) REVERT: B 696 MET cc_start: 0.9068 (mmp) cc_final: 0.8635 (mmp) REVERT: B 757 MET cc_start: 0.9046 (mtt) cc_final: 0.8433 (mmp) REVERT: B 906 MET cc_start: 0.9536 (mmp) cc_final: 0.8785 (pmm) REVERT: B 913 MET cc_start: 0.9489 (mtm) cc_final: 0.9177 (mtp) REVERT: B 939 MET cc_start: 0.8764 (ptm) cc_final: 0.8094 (ptp) REVERT: B 943 MET cc_start: 0.9337 (mmm) cc_final: 0.8561 (mmm) REVERT: B 1008 MET cc_start: 0.9324 (ppp) cc_final: 0.9041 (tmm) REVERT: C 84 MET cc_start: 0.9649 (tpt) cc_final: 0.9408 (tpt) REVERT: C 278 MET cc_start: 0.8003 (mmp) cc_final: 0.7552 (mmp) REVERT: C 757 MET cc_start: 0.9560 (tpt) cc_final: 0.8920 (tpp) REVERT: C 943 MET cc_start: 0.9404 (tpt) cc_final: 0.9199 (tpt) REVERT: C 1137 MET cc_start: 0.9149 (mpp) cc_final: 0.8903 (mpp) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.1442 time to fit residues: 20.6986 Evaluate side-chains 72 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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: 40.0000 chunk 32 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 201 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 chunk 252 optimal weight: 0.9990 chunk 224 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 292 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.027682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020796 restraints weight = 547611.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.020945 restraints weight = 361169.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.021252 restraints weight = 267923.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.021483 restraints weight = 220356.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.021589 restraints weight = 191585.502| |-----------------------------------------------------------------------------| r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28632 Z= 0.159 Angle : 0.648 21.608 39087 Z= 0.315 Chirality : 0.043 0.454 4527 Planarity : 0.005 0.163 4944 Dihedral : 8.786 105.975 5067 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 0.07 % Allowed : 2.92 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.14), residues: 3462 helix: 1.32 (0.20), residues: 690 sheet: -0.79 (0.19), residues: 705 loop : -1.12 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 841 TYR 0.016 0.002 TYR A 689 PHE 0.021 0.001 PHE A 972 TRP 0.008 0.001 TRP C 310 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00329 (28521) covalent geometry : angle 0.60213 (38802) SS BOND : bond 0.00357 ( 48) SS BOND : angle 1.39763 ( 96) hydrogen bonds : bond 0.03478 ( 1021) hydrogen bonds : angle 5.80733 ( 2712) link_ALPHA1-3 : bond 0.00776 ( 3) link_ALPHA1-3 : angle 3.74410 ( 9) link_ALPHA1-6 : bond 0.00709 ( 3) link_ALPHA1-6 : angle 1.45866 ( 9) link_BETA1-4 : bond 0.00615 ( 18) link_BETA1-4 : angle 2.37567 ( 54) link_BETA1-6 : bond 0.01189 ( 6) link_BETA1-6 : angle 2.78779 ( 18) link_NAG-ASN : bond 0.00777 ( 33) link_NAG-ASN : angle 3.96835 ( 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 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8367 (mmt) cc_final: 0.8146 (mmm) REVERT: A 278 MET cc_start: 0.8967 (tpp) cc_final: 0.8698 (tpp) REVERT: A 296 ILE cc_start: 0.9415 (mp) cc_final: 0.8971 (mp) REVERT: A 686 MET cc_start: 0.8209 (mmp) cc_final: 0.7957 (mmm) REVERT: A 696 MET cc_start: 0.8565 (mmt) cc_final: 0.8193 (mmm) REVERT: A 939 MET cc_start: 0.9526 (tpp) cc_final: 0.9260 (tpp) REVERT: B 278 MET cc_start: 0.8601 (tpt) cc_final: 0.8021 (tpp) REVERT: B 292 TYR cc_start: 0.9655 (m-80) cc_final: 0.9344 (m-80) REVERT: B 696 MET cc_start: 0.9028 (mmp) cc_final: 0.8581 (mmp) REVERT: B 757 MET cc_start: 0.9070 (mtt) cc_final: 0.8453 (mmp) REVERT: B 906 MET cc_start: 0.9515 (mmp) cc_final: 0.8720 (pmm) REVERT: B 913 MET cc_start: 0.9474 (mtm) cc_final: 0.9133 (mtp) REVERT: B 939 MET cc_start: 0.8920 (ptm) cc_final: 0.8157 (ptp) REVERT: B 943 MET cc_start: 0.9343 (mmm) cc_final: 0.8493 (mmm) REVERT: B 1008 MET cc_start: 0.9331 (ppp) cc_final: 0.9018 (tmm) REVERT: C 278 MET cc_start: 0.8017 (mmp) cc_final: 0.7593 (mmp) REVERT: C 757 MET cc_start: 0.9537 (tpt) cc_final: 0.8919 (tpp) REVERT: C 943 MET cc_start: 0.9318 (tpt) cc_final: 0.9051 (tpt) REVERT: C 1137 MET cc_start: 0.9097 (mpp) cc_final: 0.8846 (mpp) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.1357 time to fit residues: 19.1211 Evaluate side-chains 70 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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: 8.9990 chunk 322 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 290 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** 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** A1212 GLN B 72 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 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 522 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.026947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.020061 restraints weight = 555171.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.020213 restraints weight = 371884.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.020497 restraints weight = 278462.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.020719 restraints weight = 230034.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.020840 restraints weight = 202432.584| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28632 Z= 0.202 Angle : 0.683 21.855 39087 Z= 0.336 Chirality : 0.044 0.434 4527 Planarity : 0.004 0.118 4944 Dihedral : 8.744 109.708 5067 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % 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 aren not related in a simple way. whole: -0.78 (0.14), residues: 3462 helix: 1.45 (0.20), residues: 680 sheet: -0.83 (0.19), residues: 686 loop : -1.10 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 694 TYR 0.020 0.002 TYR C 314 PHE 0.025 0.002 PHE A1136 TRP 0.010 0.001 TRP B 310 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00409 (28521) covalent geometry : angle 0.64071 (38802) SS BOND : bond 0.00339 ( 48) SS BOND : angle 1.35523 ( 96) hydrogen bonds : bond 0.03708 ( 1021) hydrogen bonds : angle 5.95055 ( 2712) link_ALPHA1-3 : bond 0.00658 ( 3) link_ALPHA1-3 : angle 3.79343 ( 9) link_ALPHA1-6 : bond 0.00716 ( 3) link_ALPHA1-6 : angle 1.53264 ( 9) link_BETA1-4 : bond 0.00769 ( 18) link_BETA1-4 : angle 2.47902 ( 54) link_BETA1-6 : bond 0.01239 ( 6) link_BETA1-6 : angle 2.82293 ( 18) link_NAG-ASN : bond 0.00713 ( 33) link_NAG-ASN : angle 3.91464 ( 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 82 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8478 (mmt) cc_final: 0.8255 (mmm) REVERT: A 278 MET cc_start: 0.8873 (tpp) cc_final: 0.8621 (tpp) REVERT: A 296 ILE cc_start: 0.9421 (mp) cc_final: 0.9024 (mp) REVERT: A 686 MET cc_start: 0.8371 (mmp) cc_final: 0.8150 (mmm) REVERT: A 696 MET cc_start: 0.8275 (mmt) cc_final: 0.8017 (mmp) REVERT: A 757 MET cc_start: 0.7797 (tpp) cc_final: 0.7498 (tpp) REVERT: A 939 MET cc_start: 0.9564 (tpp) cc_final: 0.8957 (ttt) REVERT: B 147 PHE cc_start: 0.9518 (m-80) cc_final: 0.9186 (m-10) REVERT: B 278 MET cc_start: 0.8498 (tpt) cc_final: 0.7900 (tpp) REVERT: B 292 TYR cc_start: 0.9680 (m-80) cc_final: 0.9382 (m-80) REVERT: B 696 MET cc_start: 0.9017 (mmp) cc_final: 0.8569 (mmp) REVERT: B 757 MET cc_start: 0.9092 (mtt) cc_final: 0.8482 (mmp) REVERT: B 906 MET cc_start: 0.9525 (mmp) cc_final: 0.8777 (pmm) REVERT: B 913 MET cc_start: 0.9516 (mtm) cc_final: 0.9231 (mtp) REVERT: B 939 MET cc_start: 0.8999 (ptm) cc_final: 0.8395 (ptp) REVERT: B 943 MET cc_start: 0.9316 (mmm) cc_final: 0.8585 (mmm) REVERT: C 278 MET cc_start: 0.8069 (mmp) cc_final: 0.7674 (mmp) REVERT: C 757 MET cc_start: 0.9524 (tpt) cc_final: 0.8937 (tpp) REVERT: C 1137 MET cc_start: 0.9134 (mpp) cc_final: 0.8874 (mpp) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1392 time to fit residues: 19.8078 Evaluate side-chains 70 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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: 10.0000 chunk 256 optimal weight: 1.9990 chunk 171 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 303 optimal weight: 40.0000 chunk 118 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** 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 B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS B1169 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.020494 restraints weight = 547960.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.020679 restraints weight = 359636.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.020977 restraints weight = 266691.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.021219 restraints weight = 219711.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.021381 restraints weight = 192425.114| |-----------------------------------------------------------------------------| r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3333 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= 0.141 Angle : 0.645 21.548 39087 Z= 0.313 Chirality : 0.044 0.433 4527 Planarity : 0.004 0.092 4944 Dihedral : 8.280 105.311 5067 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.07 % Allowed : 1.60 % Favored : 98.34 % 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 aren not related in a simple way. whole: -0.69 (0.14), residues: 3462 helix: 1.48 (0.20), residues: 700 sheet: -0.61 (0.19), residues: 663 loop : -1.11 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 841 TYR 0.020 0.001 TYR B 609 PHE 0.024 0.001 PHE B 164 TRP 0.007 0.001 TRP B 310 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00303 (28521) covalent geometry : angle 0.60063 (38802) SS BOND : bond 0.00368 ( 48) SS BOND : angle 1.66187 ( 96) hydrogen bonds : bond 0.03362 ( 1021) hydrogen bonds : angle 5.78191 ( 2712) link_ALPHA1-3 : bond 0.00885 ( 3) link_ALPHA1-3 : angle 3.32152 ( 9) link_ALPHA1-6 : bond 0.00798 ( 3) link_ALPHA1-6 : angle 1.47226 ( 9) link_BETA1-4 : bond 0.00679 ( 18) link_BETA1-4 : angle 2.29747 ( 54) link_BETA1-6 : bond 0.01299 ( 6) link_BETA1-6 : angle 3.13920 ( 18) link_NAG-ASN : bond 0.00705 ( 33) link_NAG-ASN : angle 3.80854 ( 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 81 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8414 (mmt) cc_final: 0.8193 (mmm) REVERT: A 278 MET cc_start: 0.8782 (tpp) cc_final: 0.8527 (tpp) REVERT: A 296 ILE cc_start: 0.9339 (mp) cc_final: 0.9000 (mp) REVERT: A 686 MET cc_start: 0.8231 (mmp) cc_final: 0.8021 (mmm) REVERT: A 696 MET cc_start: 0.8290 (mmt) cc_final: 0.8037 (mmp) REVERT: A 757 MET cc_start: 0.7763 (tpp) cc_final: 0.7544 (tpp) REVERT: A 939 MET cc_start: 0.9595 (tpp) cc_final: 0.9378 (tpt) REVERT: B 147 PHE cc_start: 0.9487 (m-80) cc_final: 0.9255 (m-10) REVERT: B 148 MET cc_start: 0.9689 (tmm) cc_final: 0.9369 (ppp) REVERT: B 278 MET cc_start: 0.8563 (tpt) cc_final: 0.7771 (tpp) REVERT: B 292 TYR cc_start: 0.9670 (m-80) cc_final: 0.9365 (m-80) REVERT: B 696 MET cc_start: 0.8994 (mmp) cc_final: 0.8540 (mmp) REVERT: B 757 MET cc_start: 0.9132 (mtt) cc_final: 0.8553 (mmp) REVERT: B 906 MET cc_start: 0.9513 (mmp) cc_final: 0.8787 (pmm) REVERT: B 913 MET cc_start: 0.9486 (mtm) cc_final: 0.9191 (mtp) REVERT: B 939 MET cc_start: 0.8964 (ptm) cc_final: 0.8262 (ptp) REVERT: B 943 MET cc_start: 0.9299 (mmm) cc_final: 0.8344 (mmm) REVERT: C 278 MET cc_start: 0.8013 (mmp) cc_final: 0.7626 (mmp) REVERT: C 757 MET cc_start: 0.9503 (tpt) cc_final: 0.8908 (tpp) REVERT: C 1137 MET cc_start: 0.9169 (mpp) cc_final: 0.8878 (mpp) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.1405 time to fit residues: 19.7954 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 : 0.797 ------------------------------------------------------------------------------- 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: 50.0000 chunk 212 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 342 optimal weight: 10.0000 chunk 316 optimal weight: 0.0040 chunk 226 optimal weight: 9.9990 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: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS A 466 GLN ** 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** ** A1063 GLN ** 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.027133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.020237 restraints weight = 554599.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.020412 restraints weight = 366689.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.020712 restraints weight = 273214.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.020952 restraints weight = 224932.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.021073 restraints weight = 198049.257| |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28632 Z= 0.160 Angle : 0.655 21.744 39087 Z= 0.318 Chirality : 0.044 0.424 4527 Planarity : 0.004 0.056 4944 Dihedral : 7.903 95.802 5067 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.14), residues: 3462 helix: 1.58 (0.20), residues: 694 sheet: -0.67 (0.19), residues: 667 loop : -1.11 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 691 TYR 0.017 0.002 TYR B 609 PHE 0.025 0.002 PHE B 164 TRP 0.010 0.001 TRP C 310 HIS 0.005 0.001 HIS B1122 Details of bonding type rmsd covalent geometry : bond 0.00338 (28521) covalent geometry : angle 0.61023 (38802) SS BOND : bond 0.00392 ( 48) SS BOND : angle 1.55511 ( 96) hydrogen bonds : bond 0.03414 ( 1021) hydrogen bonds : angle 5.81571 ( 2712) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 3.26262 ( 9) link_ALPHA1-6 : bond 0.00775 ( 3) link_ALPHA1-6 : angle 1.45806 ( 9) link_BETA1-4 : bond 0.00648 ( 18) link_BETA1-4 : angle 2.31640 ( 54) link_BETA1-6 : bond 0.01064 ( 6) link_BETA1-6 : angle 2.81674 ( 18) link_NAG-ASN : bond 0.00727 ( 33) link_NAG-ASN : angle 3.91349 ( 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 77 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8438 (mmt) cc_final: 0.8215 (mmm) REVERT: A 296 ILE cc_start: 0.9379 (mp) cc_final: 0.9052 (mp) REVERT: A 686 MET cc_start: 0.8269 (mmp) cc_final: 0.8057 (mmm) REVERT: A 696 MET cc_start: 0.8311 (mmt) cc_final: 0.8069 (mmp) REVERT: A 939 MET cc_start: 0.9601 (tpp) cc_final: 0.9371 (tpt) REVERT: B 147 PHE cc_start: 0.9491 (m-80) cc_final: 0.9232 (m-10) REVERT: B 148 MET cc_start: 0.9686 (tmm) cc_final: 0.9432 (ppp) REVERT: B 278 MET cc_start: 0.8440 (tpt) cc_final: 0.7729 (tpp) REVERT: B 292 TYR cc_start: 0.9677 (m-80) cc_final: 0.9384 (m-80) REVERT: B 696 MET cc_start: 0.8991 (mmp) cc_final: 0.8538 (mmp) REVERT: B 757 MET cc_start: 0.9130 (mtt) cc_final: 0.8604 (mmp) REVERT: B 906 MET cc_start: 0.9525 (mmp) cc_final: 0.8780 (pmm) REVERT: B 913 MET cc_start: 0.9469 (mtm) cc_final: 0.9113 (mtp) REVERT: B 943 MET cc_start: 0.9296 (mmm) cc_final: 0.8482 (tpt) REVERT: C 161 MET cc_start: 0.8705 (mmp) cc_final: 0.8447 (mmp) REVERT: C 278 MET cc_start: 0.8093 (mmp) cc_final: 0.7701 (mmp) REVERT: C 757 MET cc_start: 0.9488 (tpt) cc_final: 0.8900 (tpp) REVERT: C 1137 MET cc_start: 0.9191 (mpp) cc_final: 0.8921 (mpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1347 time to fit residues: 18.0428 Evaluate side-chains 67 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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: 30.0000 chunk 161 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 263 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 96 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 306 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 466 GLN ** 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** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 377 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** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.025956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.019138 restraints weight = 574087.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.019257 restraints weight = 388206.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.019542 restraints weight = 290023.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.019758 restraints weight = 238473.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.019842 restraints weight = 210625.800| |-----------------------------------------------------------------------------| r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 28632 Z= 0.276 Angle : 0.771 22.343 39087 Z= 0.384 Chirality : 0.045 0.409 4527 Planarity : 0.005 0.053 4944 Dihedral : 8.152 101.294 5067 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.14), residues: 3462 helix: 1.12 (0.20), residues: 702 sheet: -1.08 (0.19), residues: 664 loop : -1.24 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 691 TYR 0.024 0.003 TYR C 314 PHE 0.037 0.003 PHE B 164 TRP 0.014 0.002 TRP A 44 HIS 0.007 0.002 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00553 (28521) covalent geometry : angle 0.73286 (38802) SS BOND : bond 0.00481 ( 48) SS BOND : angle 1.71862 ( 96) hydrogen bonds : bond 0.04217 ( 1021) hydrogen bonds : angle 6.28840 ( 2712) link_ALPHA1-3 : bond 0.00913 ( 3) link_ALPHA1-3 : angle 3.27710 ( 9) link_ALPHA1-6 : bond 0.00597 ( 3) link_ALPHA1-6 : angle 1.61835 ( 9) link_BETA1-4 : bond 0.00544 ( 18) link_BETA1-4 : angle 2.33941 ( 54) link_BETA1-6 : bond 0.01095 ( 6) link_BETA1-6 : angle 2.78353 ( 18) link_NAG-ASN : bond 0.00699 ( 33) link_NAG-ASN : angle 3.97965 ( 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 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8433 (mmt) cc_final: 0.8212 (mmm) REVERT: A 169 LEU cc_start: 0.9805 (tp) cc_final: 0.9507 (pp) REVERT: A 278 MET cc_start: 0.9298 (tpt) cc_final: 0.8917 (tpp) REVERT: A 296 ILE cc_start: 0.9399 (mp) cc_final: 0.9142 (mp) REVERT: B 147 PHE cc_start: 0.9461 (m-80) cc_final: 0.9089 (m-10) REVERT: B 278 MET cc_start: 0.8455 (tpt) cc_final: 0.7622 (tpp) REVERT: B 696 MET cc_start: 0.8956 (mmp) cc_final: 0.8509 (mmp) REVERT: B 757 MET cc_start: 0.9165 (mtt) cc_final: 0.8763 (mtt) REVERT: B 913 MET cc_start: 0.9512 (mtm) cc_final: 0.9155 (mtp) REVERT: B 943 MET cc_start: 0.9316 (mmm) cc_final: 0.8691 (tpp) REVERT: C 148 MET cc_start: 0.9774 (ppp) cc_final: 0.9550 (ppp) REVERT: C 161 MET cc_start: 0.8671 (mmp) cc_final: 0.8469 (mmp) REVERT: C 278 MET cc_start: 0.8090 (mmp) cc_final: 0.7726 (mmp) REVERT: C 757 MET cc_start: 0.9487 (tpt) cc_final: 0.8996 (tpp) REVERT: C 943 MET cc_start: 0.9424 (tpt) cc_final: 0.9202 (tpt) REVERT: C 1137 MET cc_start: 0.9196 (mpp) cc_final: 0.8934 (mpp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.1435 time to fit residues: 18.7988 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 : 0.966 ------------------------------------------------------------------------------- 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: 6.9990 chunk 294 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 183 optimal weight: 0.8980 chunk 165 optimal weight: 9.9990 chunk 14 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 839 ASN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 GLN ** 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** C1212 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.027023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020173 restraints weight = 551982.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.020344 restraints weight = 359845.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.020643 restraints weight = 265913.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.020869 restraints weight = 216401.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.021030 restraints weight = 192918.766| |-----------------------------------------------------------------------------| r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28632 Z= 0.143 Angle : 0.687 21.692 39087 Z= 0.331 Chirality : 0.045 0.406 4527 Planarity : 0.004 0.053 4944 Dihedral : 7.821 98.764 5067 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % 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 aren not related in a simple way. whole: -0.83 (0.14), residues: 3462 helix: 1.35 (0.20), residues: 717 sheet: -0.80 (0.19), residues: 637 loop : -1.19 (0.13), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 181 TYR 0.026 0.002 TYR C 314 PHE 0.019 0.001 PHE B 164 TRP 0.014 0.001 TRP C 44 HIS 0.007 0.001 HIS C 167 Details of bonding type rmsd covalent geometry : bond 0.00309 (28521) covalent geometry : angle 0.64283 (38802) SS BOND : bond 0.00350 ( 48) SS BOND : angle 1.60287 ( 96) hydrogen bonds : bond 0.03433 ( 1021) hydrogen bonds : angle 5.87752 ( 2712) link_ALPHA1-3 : bond 0.01232 ( 3) link_ALPHA1-3 : angle 2.06021 ( 9) link_ALPHA1-6 : bond 0.00844 ( 3) link_ALPHA1-6 : angle 1.48818 ( 9) link_BETA1-4 : bond 0.00706 ( 18) link_BETA1-4 : angle 2.16976 ( 54) link_BETA1-6 : bond 0.01137 ( 6) link_BETA1-6 : angle 2.83902 ( 18) link_NAG-ASN : bond 0.00614 ( 33) link_NAG-ASN : angle 4.12444 ( 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 : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8383 (mmt) cc_final: 0.8161 (mmm) REVERT: A 278 MET cc_start: 0.9223 (tpt) cc_final: 0.8740 (tpp) REVERT: A 296 ILE cc_start: 0.9358 (mp) cc_final: 0.9128 (mp) REVERT: A 696 MET cc_start: 0.8363 (mmt) cc_final: 0.7889 (mmm) REVERT: A 939 MET cc_start: 0.9160 (tpt) cc_final: 0.8895 (tpt) REVERT: A 943 MET cc_start: 0.8976 (tpt) cc_final: 0.8473 (tpp) REVERT: B 147 PHE cc_start: 0.9503 (m-80) cc_final: 0.9257 (m-10) REVERT: B 278 MET cc_start: 0.8313 (tpt) cc_final: 0.7525 (tpp) REVERT: B 292 TYR cc_start: 0.9682 (m-80) cc_final: 0.9396 (m-80) REVERT: B 452 MET cc_start: 0.8484 (pmm) cc_final: 0.8270 (pmm) REVERT: B 696 MET cc_start: 0.9026 (mmp) cc_final: 0.8588 (mmp) REVERT: B 757 MET cc_start: 0.9081 (mtt) cc_final: 0.8787 (mmm) REVERT: B 906 MET cc_start: 0.9454 (mmp) cc_final: 0.8719 (pmm) REVERT: B 913 MET cc_start: 0.9516 (mtm) cc_final: 0.9176 (mtp) REVERT: B 943 MET cc_start: 0.9263 (mmm) cc_final: 0.8619 (tpp) REVERT: C 161 MET cc_start: 0.8638 (mmp) cc_final: 0.8375 (mmp) REVERT: C 278 MET cc_start: 0.7900 (mmp) cc_final: 0.7550 (mmp) REVERT: C 757 MET cc_start: 0.9464 (tpt) cc_final: 0.8936 (tpp) REVERT: C 943 MET cc_start: 0.9416 (tpt) cc_final: 0.9163 (tpt) REVERT: C 1137 MET cc_start: 0.9307 (mpp) cc_final: 0.9025 (mpp) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1395 time to fit residues: 18.1371 Evaluate side-chains 67 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 9.9990 chunk 172 optimal weight: 0.0170 chunk 87 optimal weight: 20.0000 chunk 275 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 30.0000 chunk 195 optimal weight: 10.0000 chunk 347 optimal weight: 0.0470 chunk 53 optimal weight: 30.0000 chunk 260 optimal weight: 8.9990 overall best weight: 2.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN B 647 ASN ** B1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 522 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.027519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.020676 restraints weight = 543797.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.020877 restraints weight = 355215.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.021182 restraints weight = 260719.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.021410 restraints weight = 213189.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.021536 restraints weight = 186246.155| |-----------------------------------------------------------------------------| r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28632 Z= 0.121 Angle : 0.648 21.481 39087 Z= 0.313 Chirality : 0.044 0.410 4527 Planarity : 0.004 0.053 4944 Dihedral : 7.355 97.301 5067 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.14), residues: 3462 helix: 1.54 (0.20), residues: 717 sheet: -0.80 (0.19), residues: 679 loop : -1.02 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.016 0.001 TYR B 85 PHE 0.015 0.001 PHE B 164 TRP 0.017 0.001 TRP C 44 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd covalent geometry : bond 0.00267 (28521) covalent geometry : angle 0.60631 (38802) SS BOND : bond 0.00298 ( 48) SS BOND : angle 1.43666 ( 96) hydrogen bonds : bond 0.03270 ( 1021) hydrogen bonds : angle 5.64255 ( 2712) link_ALPHA1-3 : bond 0.01166 ( 3) link_ALPHA1-3 : angle 1.80415 ( 9) link_ALPHA1-6 : bond 0.00865 ( 3) link_ALPHA1-6 : angle 1.47489 ( 9) link_BETA1-4 : bond 0.00740 ( 18) link_BETA1-4 : angle 2.26472 ( 54) link_BETA1-6 : bond 0.01136 ( 6) link_BETA1-6 : angle 2.76963 ( 18) link_NAG-ASN : bond 0.00639 ( 33) link_NAG-ASN : angle 3.86751 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3427.41 seconds wall clock time: 61 minutes 18.30 seconds (3678.30 seconds total)