Starting phenix.real_space_refine on Tue Jun 24 09:27:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ymz_33948/06_2025/7ymz_33948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ymz_33948/06_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_33948/06_2025/7ymz_33948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ymz_33948/06_2025/7ymz_33948.map" model { file = "/net/cci-nas-00/data/ceres_data/7ymz_33948/06_2025/7ymz_33948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ymz_33948/06_2025/7ymz_33948.cif" } resolution = 4.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.23, per 1000 atoms: 0.58 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: 7.56 Conformation dependent library (CDL) restraints added in 3.5 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 56 sheets defined 25.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 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: 14.34 Time building geometry restraints manager: 8.95 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: 0.00 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: 0.710 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: 0.040 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 68.600 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.160 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.570 ------------------------------------------------------------------------------- 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 : 7.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP C 253 HIS 0.010 0.001 HIS B 681 PHE 0.038 0.002 PHE A 254 TYR 0.027 0.002 TYR C 71 ARG 0.007 0.000 ARG B 505 Details of bonding type rmsd link_NAG-ASN : bond 0.01182 ( 33) link_NAG-ASN : angle 4.69761 ( 99) 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_ALPHA1-3 : bond 0.00256 ( 3) link_ALPHA1-3 : angle 1.93181 ( 9) hydrogen bonds : bond 0.14178 ( 1021) hydrogen bonds : angle 6.93291 ( 2712) link_BETA1-6 : bond 0.01226 ( 6) link_BETA1-6 : angle 2.87567 ( 18) SS BOND : bond 0.00209 ( 48) SS BOND : angle 1.45948 ( 96) covalent geometry : bond 0.00498 (28521) covalent geometry : angle 0.89156 (38802) *********************** 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 : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.7812 (mmt) cc_final: 0.7574 (mmm) REVERT: A 296 ILE cc_start: 0.8920 (mp) cc_final: 0.8675 (mp) REVERT: A 452 MET cc_start: 0.7393 (pmm) cc_final: 0.7040 (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: 0.7892 (mmt) REVERT: B 147 PHE cc_start: 0.8700 (m-80) cc_final: 0.8290 (m-10) REVERT: B 292 TYR cc_start: 0.8951 (m-80) cc_final: 0.8666 (m-80) REVERT: B 452 MET cc_start: 0.7381 (pmm) cc_final: 0.7084 (pmm) REVERT: B 563 MET cc_start: 0.7506 (mmt) cc_final: 0.7218 (mmt) REVERT: B 569 MET cc_start: 0.8714 (pmm) cc_final: 0.7620 (pmm) REVERT: B 686 MET cc_start: 0.6909 (mmp) cc_final: 0.6578 (mmp) REVERT: B 906 MET cc_start: 0.8562 (mmp) cc_final: 0.8249 (pmm) REVERT: B 943 MET cc_start: 0.8615 (mmm) cc_final: 0.7443 (mmm) REVERT: C 563 MET cc_start: 0.8439 (tpt) cc_final: 0.7956 (tpt) REVERT: C 635 TYR cc_start: 0.9109 (m-10) cc_final: 0.8901 (m-10) REVERT: C 695 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.8879 (p) REVERT: C 696 MET cc_start: 0.8225 (tpt) cc_final: 0.7934 (tpt) REVERT: C 757 MET cc_start: 0.8512 (tpt) cc_final: 0.8151 (tpp) outliers start: 21 outliers final: 4 residues processed: 144 average time/residue: 0.3804 time to fit residues: 90.5980 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 : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 7.9990 chunk 263 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 90 optimal weight: 40.0000 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 165 optimal weight: 0.0470 chunk 203 optimal weight: 3.9990 chunk 316 optimal weight: 9.9990 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 167 HIS ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1029 ASN B 72 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 ASN ** C 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.030215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.023253 restraints weight = 525588.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.023498 restraints weight = 344098.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.023819 restraints weight = 252772.661| |-----------------------------------------------------------------------------| r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28632 Z= 0.157 Angle : 0.659 21.994 39087 Z= 0.326 Chirality : 0.044 0.596 4527 Planarity : 0.005 0.163 4944 Dihedral : 10.757 115.005 5067 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3462 helix: 1.02 (0.20), residues: 681 sheet: -0.34 (0.19), residues: 687 loop : -1.21 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 960 HIS 0.004 0.001 HIS C1122 PHE 0.010 0.001 PHE C 399 TYR 0.014 0.001 TYR B1186 ARG 0.020 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 33) link_NAG-ASN : angle 3.68975 ( 99) link_ALPHA1-6 : bond 0.00304 ( 3) link_ALPHA1-6 : angle 1.70623 ( 9) link_BETA1-4 : bond 0.00618 ( 18) link_BETA1-4 : angle 2.47658 ( 54) link_ALPHA1-3 : bond 0.00952 ( 3) link_ALPHA1-3 : angle 4.06233 ( 9) hydrogen bonds : bond 0.03925 ( 1021) hydrogen bonds : angle 5.83518 ( 2712) link_BETA1-6 : bond 0.01057 ( 6) link_BETA1-6 : angle 2.62407 ( 18) SS BOND : bond 0.00676 ( 48) SS BOND : angle 1.35507 ( 96) covalent geometry : bond 0.00320 (28521) covalent geometry : angle 0.61816 (38802) *********************** 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 98 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 95 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8322 (mmt) cc_final: 0.8115 (mmm) REVERT: A 171 LEU cc_start: 0.9673 (tp) cc_final: 0.9450 (tp) REVERT: A 287 TYR cc_start: 0.8011 (t80) cc_final: 0.7765 (t80) REVERT: A 296 ILE cc_start: 0.9343 (mp) cc_final: 0.8930 (mp) REVERT: A 686 MET cc_start: 0.7836 (mmp) cc_final: 0.7590 (mmm) REVERT: A 939 MET cc_start: 0.9368 (tpp) cc_final: 0.9051 (tpp) REVERT: B 147 PHE cc_start: 0.9520 (m-80) cc_final: 0.9261 (m-10) REVERT: B 292 TYR cc_start: 0.9660 (m-80) cc_final: 0.9354 (m-10) REVERT: B 696 MET cc_start: 0.9090 (mmp) cc_final: 0.8547 (mmp) REVERT: B 757 MET cc_start: 0.8674 (mtt) cc_final: 0.8239 (tpp) REVERT: B 906 MET cc_start: 0.9429 (mmp) cc_final: 0.8675 (pmm) REVERT: B 913 MET cc_start: 0.9428 (mtm) cc_final: 0.9135 (mtp) REVERT: B 939 MET cc_start: 0.8320 (ptm) cc_final: 0.7681 (ptp) REVERT: B 943 MET cc_start: 0.9428 (mmm) cc_final: 0.8690 (mmm) REVERT: C 84 MET cc_start: 0.8940 (tpt) cc_final: 0.8696 (tpt) REVERT: C 563 MET cc_start: 0.9421 (tpt) cc_final: 0.9104 (tpt) REVERT: C 635 TYR cc_start: 0.9850 (m-10) cc_final: 0.9625 (m-80) REVERT: C 696 MET cc_start: 0.7806 (tpt) cc_final: 0.7325 (tpt) REVERT: C 757 MET cc_start: 0.9457 (tpt) cc_final: 0.8864 (tpp) REVERT: C 906 MET cc_start: 0.9425 (tpt) cc_final: 0.9108 (tmm) REVERT: C 943 MET cc_start: 0.9387 (tpt) cc_final: 0.9127 (tpp) REVERT: C 1137 MET cc_start: 0.9035 (mpp) cc_final: 0.8758 (mpp) outliers start: 3 outliers final: 0 residues processed: 98 average time/residue: 0.3891 time to fit residues: 65.5193 Evaluate side-chains 78 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 59 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 chunk 266 optimal weight: 20.0000 chunk 138 optimal weight: 50.0000 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 329 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 236 optimal weight: 30.0000 chunk 174 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 796 GLN A 907 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 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 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN C 522 GLN C 842 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.028395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.021509 restraints weight = 546218.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.021693 restraints weight = 361596.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.021985 restraints weight = 266137.580| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28632 Z= 0.201 Angle : 0.682 21.738 39087 Z= 0.339 Chirality : 0.044 0.499 4527 Planarity : 0.005 0.199 4944 Dihedral : 9.429 112.324 5067 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.88 % Rotamer: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.14), residues: 3462 helix: 1.35 (0.20), residues: 679 sheet: -0.51 (0.19), residues: 696 loop : -1.14 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 960 HIS 0.006 0.001 HIS A 264 PHE 0.030 0.002 PHE A 972 TYR 0.020 0.002 TYR A 64 ARG 0.011 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 33) link_NAG-ASN : angle 3.86491 ( 99) link_ALPHA1-6 : bond 0.00641 ( 3) link_ALPHA1-6 : angle 1.63069 ( 9) link_BETA1-4 : bond 0.00592 ( 18) link_BETA1-4 : angle 2.36629 ( 54) link_ALPHA1-3 : bond 0.00683 ( 3) link_ALPHA1-3 : angle 3.75083 ( 9) hydrogen bonds : bond 0.03815 ( 1021) hydrogen bonds : angle 5.87848 ( 2712) link_BETA1-6 : bond 0.01090 ( 6) link_BETA1-6 : angle 2.55680 ( 18) SS BOND : bond 0.00393 ( 48) SS BOND : angle 1.47014 ( 96) covalent geometry : bond 0.00409 (28521) covalent geometry : angle 0.64036 (38802) *********************** 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 93 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8422 (mmt) cc_final: 0.8220 (mmm) REVERT: A 296 ILE cc_start: 0.9460 (mp) cc_final: 0.8965 (mp) REVERT: A 686 MET cc_start: 0.8222 (mmp) cc_final: 0.7963 (mmm) REVERT: A 696 MET cc_start: 0.8538 (mmt) cc_final: 0.7964 (mmp) REVERT: A 757 MET cc_start: 0.7895 (tpp) cc_final: 0.7579 (tpp) REVERT: A 906 MET cc_start: 0.8742 (mmm) cc_final: 0.8539 (mmm) REVERT: A 939 MET cc_start: 0.9495 (tpp) cc_final: 0.9226 (tpp) REVERT: B 147 PHE cc_start: 0.9511 (m-80) cc_final: 0.9174 (m-10) REVERT: B 278 MET cc_start: 0.8957 (tpt) cc_final: 0.8117 (tpp) REVERT: B 292 TYR cc_start: 0.9701 (m-80) cc_final: 0.9379 (m-80) REVERT: B 696 MET cc_start: 0.8999 (mmp) cc_final: 0.8501 (mmp) REVERT: B 757 MET cc_start: 0.8893 (mtt) cc_final: 0.8351 (tpp) REVERT: B 906 MET cc_start: 0.9531 (mmp) cc_final: 0.8776 (pmm) REVERT: B 913 MET cc_start: 0.9469 (mtm) cc_final: 0.9161 (mtp) REVERT: B 939 MET cc_start: 0.8697 (ptm) cc_final: 0.7906 (ptp) REVERT: B 943 MET cc_start: 0.9422 (mmm) cc_final: 0.8578 (mmm) REVERT: C 84 MET cc_start: 0.9447 (tpt) cc_final: 0.9171 (tpt) REVERT: C 635 TYR cc_start: 0.9822 (m-10) cc_final: 0.9598 (m-10) REVERT: C 696 MET cc_start: 0.7874 (tpt) cc_final: 0.7606 (tpt) REVERT: C 757 MET cc_start: 0.9543 (tpt) cc_final: 0.8927 (tpp) REVERT: C 906 MET cc_start: 0.9532 (tpt) cc_final: 0.9252 (tmm) REVERT: C 1137 MET cc_start: 0.9057 (mpp) cc_final: 0.8762 (mpp) outliers start: 2 outliers final: 0 residues processed: 93 average time/residue: 0.3903 time to fit residues: 63.0430 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 : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 104 optimal weight: 6.9990 chunk 44 optimal weight: 40.0000 chunk 248 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 287 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 234 optimal weight: 1.9990 chunk 40 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 336 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 842 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1084 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 = 0.2797 r_free = 0.2797 target = 0.028544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.021568 restraints weight = 540813.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.021793 restraints weight = 354581.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.022101 restraints weight = 262147.621| |-----------------------------------------------------------------------------| r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2289 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= 0.151 Angle : 0.636 21.290 39087 Z= 0.310 Chirality : 0.044 0.487 4527 Planarity : 0.005 0.144 4944 Dihedral : 9.012 112.775 5067 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.14), residues: 3462 helix: 1.45 (0.20), residues: 683 sheet: -0.65 (0.18), residues: 747 loop : -1.08 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.004 0.001 HIS B 836 PHE 0.026 0.001 PHE A 972 TYR 0.021 0.002 TYR A 609 ARG 0.018 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00637 ( 33) link_NAG-ASN : angle 3.85587 ( 99) link_ALPHA1-6 : bond 0.00743 ( 3) link_ALPHA1-6 : angle 1.47678 ( 9) link_BETA1-4 : bond 0.00692 ( 18) link_BETA1-4 : angle 2.37846 ( 54) link_ALPHA1-3 : bond 0.00865 ( 3) link_ALPHA1-3 : angle 3.68165 ( 9) hydrogen bonds : bond 0.03420 ( 1021) hydrogen bonds : angle 5.71446 ( 2712) link_BETA1-6 : bond 0.01191 ( 6) link_BETA1-6 : angle 2.78176 ( 18) SS BOND : bond 0.00307 ( 48) SS BOND : angle 1.52110 ( 96) covalent geometry : bond 0.00316 (28521) covalent geometry : angle 0.59059 (38802) *********************** 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 90 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8426 (mmt) cc_final: 0.8217 (mmm) REVERT: A 278 MET cc_start: 0.9163 (tpp) cc_final: 0.8923 (tpp) REVERT: A 296 ILE cc_start: 0.9391 (mp) cc_final: 0.8883 (mp) REVERT: A 686 MET cc_start: 0.8289 (mmp) cc_final: 0.8032 (mmm) REVERT: A 757 MET cc_start: 0.7905 (tpp) cc_final: 0.7701 (tpp) REVERT: A 906 MET cc_start: 0.8642 (mmm) cc_final: 0.8422 (mmm) REVERT: A 939 MET cc_start: 0.9534 (tpp) cc_final: 0.9261 (tpp) REVERT: B 147 PHE cc_start: 0.9536 (m-80) cc_final: 0.9288 (m-10) REVERT: B 278 MET cc_start: 0.8907 (tpt) cc_final: 0.8141 (tpp) REVERT: B 292 TYR cc_start: 0.9710 (m-80) cc_final: 0.9386 (m-80) REVERT: B 696 MET cc_start: 0.9026 (mmp) cc_final: 0.8549 (mmp) REVERT: B 757 MET cc_start: 0.9020 (mtt) cc_final: 0.8416 (tpp) REVERT: B 906 MET cc_start: 0.9510 (mmp) cc_final: 0.8779 (pmm) REVERT: B 913 MET cc_start: 0.9477 (mtm) cc_final: 0.9165 (mtp) REVERT: B 939 MET cc_start: 0.8794 (ptm) cc_final: 0.8000 (ptp) REVERT: B 943 MET cc_start: 0.9398 (mmm) cc_final: 0.8410 (mmm) REVERT: C 84 MET cc_start: 0.9552 (tpt) cc_final: 0.9208 (tpt) REVERT: C 635 TYR cc_start: 0.9834 (m-10) cc_final: 0.9621 (m-10) REVERT: C 696 MET cc_start: 0.8011 (tpt) cc_final: 0.7803 (tpt) REVERT: C 757 MET cc_start: 0.9546 (tpt) cc_final: 0.8937 (tpp) REVERT: C 906 MET cc_start: 0.9521 (tpt) cc_final: 0.9236 (tmm) REVERT: C 1137 MET cc_start: 0.9109 (mpp) cc_final: 0.8906 (mpp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.3793 time to fit residues: 58.0714 Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 319 optimal weight: 0.2980 chunk 83 optimal weight: 20.0000 chunk 121 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 316 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 218 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 126 optimal weight: 30.0000 chunk 86 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 796 GLN B 72 GLN B 226 ASN ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN C 226 ASN C 522 GLN C 708 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1084 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.028891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.021923 restraints weight = 531542.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.022149 restraints weight = 346193.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.022465 restraints weight = 255398.327| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28632 Z= 0.116 Angle : 0.615 21.048 39087 Z= 0.296 Chirality : 0.044 0.481 4527 Planarity : 0.004 0.142 4944 Dihedral : 8.499 110.490 5067 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3462 helix: 1.53 (0.20), residues: 682 sheet: -0.54 (0.19), residues: 734 loop : -1.00 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.002 0.001 HIS A 264 PHE 0.023 0.001 PHE A 972 TYR 0.025 0.001 TYR C 947 ARG 0.016 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00668 ( 33) link_NAG-ASN : angle 3.78232 ( 99) link_ALPHA1-6 : bond 0.00832 ( 3) link_ALPHA1-6 : angle 1.42682 ( 9) link_BETA1-4 : bond 0.00684 ( 18) link_BETA1-4 : angle 2.31962 ( 54) link_ALPHA1-3 : bond 0.00978 ( 3) link_ALPHA1-3 : angle 3.27407 ( 9) hydrogen bonds : bond 0.03233 ( 1021) hydrogen bonds : angle 5.51285 ( 2712) link_BETA1-6 : bond 0.01299 ( 6) link_BETA1-6 : angle 2.82975 ( 18) SS BOND : bond 0.00229 ( 48) SS BOND : angle 1.37562 ( 96) covalent geometry : bond 0.00252 (28521) covalent geometry : angle 0.57090 (38802) *********************** 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 90 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8387 (mmt) cc_final: 0.8179 (mmm) REVERT: A 296 ILE cc_start: 0.9395 (mp) cc_final: 0.8951 (mp) REVERT: A 686 MET cc_start: 0.8104 (mmp) cc_final: 0.7843 (mmm) REVERT: A 696 MET cc_start: 0.8312 (mmt) cc_final: 0.7852 (mmm) REVERT: A 757 MET cc_start: 0.7844 (tpp) cc_final: 0.7640 (tpp) REVERT: A 939 MET cc_start: 0.9546 (tpp) cc_final: 0.9296 (tpp) REVERT: B 147 PHE cc_start: 0.9518 (m-80) cc_final: 0.9283 (m-10) REVERT: B 278 MET cc_start: 0.8701 (tpt) cc_final: 0.8039 (tpp) REVERT: B 292 TYR cc_start: 0.9695 (m-80) cc_final: 0.9360 (m-80) REVERT: B 696 MET cc_start: 0.9032 (mmp) cc_final: 0.8555 (mmp) REVERT: B 757 MET cc_start: 0.9048 (mtt) cc_final: 0.8471 (tpp) REVERT: B 906 MET cc_start: 0.9548 (mmp) cc_final: 0.8791 (pmm) REVERT: B 913 MET cc_start: 0.9484 (mtm) cc_final: 0.9183 (mtp) REVERT: B 939 MET cc_start: 0.8775 (ptm) cc_final: 0.8005 (ptp) REVERT: B 943 MET cc_start: 0.9378 (mmm) cc_final: 0.8324 (mmm) REVERT: C 635 TYR cc_start: 0.9833 (m-10) cc_final: 0.9605 (m-10) REVERT: C 757 MET cc_start: 0.9567 (tpt) cc_final: 0.8929 (tpp) REVERT: C 906 MET cc_start: 0.9572 (tpt) cc_final: 0.9313 (tmm) REVERT: C 943 MET cc_start: 0.9325 (tpt) cc_final: 0.9114 (tpt) REVERT: C 1137 MET cc_start: 0.9190 (mpp) cc_final: 0.8977 (mpp) outliers start: 3 outliers final: 1 residues processed: 90 average time/residue: 0.3913 time to fit residues: 61.3886 Evaluate side-chains 74 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 77 optimal weight: 8.9990 chunk 185 optimal weight: 8.9990 chunk 172 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 311 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 51 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 chunk 308 optimal weight: 6.9990 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 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 792 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 733 GLN ** C1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.028080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.021166 restraints weight = 544489.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.021377 restraints weight = 358983.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.021683 restraints weight = 266071.186| |-----------------------------------------------------------------------------| r_work (final): 0.2432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2706 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= 0.158 Angle : 0.633 21.351 39087 Z= 0.307 Chirality : 0.043 0.461 4527 Planarity : 0.004 0.116 4944 Dihedral : 8.058 100.567 5067 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3462 helix: 1.59 (0.20), residues: 685 sheet: -0.60 (0.19), residues: 735 loop : -1.01 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.006 0.001 HIS A 264 PHE 0.023 0.001 PHE A1136 TYR 0.021 0.001 TYR C 184 ARG 0.017 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00580 ( 33) link_NAG-ASN : angle 3.81447 ( 99) link_ALPHA1-6 : bond 0.00752 ( 3) link_ALPHA1-6 : angle 1.44335 ( 9) link_BETA1-4 : bond 0.00601 ( 18) link_BETA1-4 : angle 2.36764 ( 54) link_ALPHA1-3 : bond 0.00821 ( 3) link_ALPHA1-3 : angle 3.59421 ( 9) hydrogen bonds : bond 0.03362 ( 1021) hydrogen bonds : angle 5.55833 ( 2712) link_BETA1-6 : bond 0.01075 ( 6) link_BETA1-6 : angle 3.06505 ( 18) SS BOND : bond 0.00327 ( 48) SS BOND : angle 1.35727 ( 96) covalent geometry : bond 0.00329 (28521) covalent geometry : angle 0.58878 (38802) *********************** 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 86 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8464 (mmt) cc_final: 0.8264 (mmm) REVERT: A 278 MET cc_start: 0.9503 (tpt) cc_final: 0.9055 (tpp) REVERT: A 296 ILE cc_start: 0.9369 (mp) cc_final: 0.8932 (mp) REVERT: A 686 MET cc_start: 0.8363 (mmp) cc_final: 0.8078 (mmm) REVERT: A 939 MET cc_start: 0.9550 (tpp) cc_final: 0.8844 (ttt) REVERT: A 943 MET cc_start: 0.9228 (mmm) cc_final: 0.9027 (tpp) REVERT: B 147 PHE cc_start: 0.9559 (m-80) cc_final: 0.9307 (m-10) REVERT: B 278 MET cc_start: 0.8628 (tpt) cc_final: 0.7866 (tpp) REVERT: B 292 TYR cc_start: 0.9703 (m-80) cc_final: 0.9375 (m-80) REVERT: B 696 MET cc_start: 0.9009 (mmp) cc_final: 0.8522 (mmp) REVERT: B 757 MET cc_start: 0.9084 (mtt) cc_final: 0.8714 (mtt) REVERT: B 906 MET cc_start: 0.9562 (mmp) cc_final: 0.8796 (pmm) REVERT: B 913 MET cc_start: 0.9462 (mtm) cc_final: 0.9203 (mtp) REVERT: B 939 MET cc_start: 0.8818 (ptm) cc_final: 0.8051 (ptp) REVERT: B 943 MET cc_start: 0.9381 (mmm) cc_final: 0.8331 (mmm) REVERT: C 84 MET cc_start: 0.9711 (mmm) cc_final: 0.9377 (tpt) REVERT: C 757 MET cc_start: 0.9598 (tpt) cc_final: 0.8965 (tpp) REVERT: C 906 MET cc_start: 0.9587 (tpt) cc_final: 0.9351 (tmm) REVERT: C 943 MET cc_start: 0.9418 (tpt) cc_final: 0.9129 (tpt) REVERT: C 1137 MET cc_start: 0.9133 (mpp) cc_final: 0.8919 (mpp) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.4326 time to fit residues: 65.5663 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 : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 194 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 50.0000 chunk 160 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 162 optimal weight: 40.0000 chunk 54 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 275 optimal weight: 0.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 398 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 B1122 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 ASN ** C1029 ASN ** 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 = 0.2763 r_free = 0.2763 target = 0.027228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.020365 restraints weight = 553639.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.020544 restraints weight = 368146.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.020850 restraints weight = 275371.686| |-----------------------------------------------------------------------------| r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28632 Z= 0.196 Angle : 0.669 21.569 39087 Z= 0.329 Chirality : 0.044 0.446 4527 Planarity : 0.004 0.067 4944 Dihedral : 8.058 106.459 5067 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3462 helix: 1.55 (0.20), residues: 693 sheet: -0.68 (0.19), residues: 724 loop : -1.06 (0.14), residues: 2045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 310 HIS 0.006 0.001 HIS A1138 PHE 0.038 0.002 PHE B 164 TYR 0.021 0.002 TYR C 184 ARG 0.014 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00582 ( 33) link_NAG-ASN : angle 3.74399 ( 99) link_ALPHA1-6 : bond 0.00676 ( 3) link_ALPHA1-6 : angle 1.53314 ( 9) link_BETA1-4 : bond 0.00587 ( 18) link_BETA1-4 : angle 2.29397 ( 54) link_ALPHA1-3 : bond 0.00848 ( 3) link_ALPHA1-3 : angle 3.52479 ( 9) hydrogen bonds : bond 0.03566 ( 1021) hydrogen bonds : angle 5.77372 ( 2712) link_BETA1-6 : bond 0.00936 ( 6) link_BETA1-6 : angle 2.77758 ( 18) SS BOND : bond 0.00352 ( 48) SS BOND : angle 1.61184 ( 96) covalent geometry : bond 0.00402 (28521) covalent geometry : angle 0.62806 (38802) *********************** 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: 0 poor density : 81 time to evaluate : 3.198 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: 0.8462 (mmt) cc_final: 0.8253 (mmm) REVERT: A 278 MET cc_start: 0.9400 (tpt) cc_final: 0.8881 (tpp) REVERT: A 296 ILE cc_start: 0.9343 (mp) cc_final: 0.8966 (mp) REVERT: A 686 MET cc_start: 0.8339 (mmp) cc_final: 0.8091 (mmm) REVERT: A 696 MET cc_start: 0.8365 (mmt) cc_final: 0.8012 (mmm) REVERT: A 939 MET cc_start: 0.9578 (tpp) cc_final: 0.9348 (tpp) REVERT: B 148 MET cc_start: 0.9500 (ppp) cc_final: 0.9264 (ppp) REVERT: B 278 MET cc_start: 0.8687 (tpt) cc_final: 0.7636 (tpp) REVERT: B 292 TYR cc_start: 0.9683 (m-80) cc_final: 0.9354 (m-80) REVERT: B 696 MET cc_start: 0.8961 (mmp) cc_final: 0.8474 (mmp) REVERT: B 757 MET cc_start: 0.9120 (mtt) cc_final: 0.8422 (mmm) REVERT: B 906 MET cc_start: 0.9581 (mmp) cc_final: 0.8831 (pmm) REVERT: B 913 MET cc_start: 0.9470 (mtm) cc_final: 0.9224 (mtp) REVERT: B 943 MET cc_start: 0.9327 (mmm) cc_final: 0.8612 (tpt) REVERT: C 757 MET cc_start: 0.9560 (tpt) cc_final: 0.8919 (tpp) REVERT: C 1137 MET cc_start: 0.9169 (mpp) cc_final: 0.8959 (mpp) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.4903 time to fit residues: 70.4721 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 : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 55 optimal weight: 7.9990 chunk 181 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 259 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 133 optimal weight: 40.0000 chunk 28 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 164 optimal weight: 30.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B1122 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** 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 = 0.2776 r_free = 0.2776 target = 0.027483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.020561 restraints weight = 549614.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.020762 restraints weight = 360544.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.021082 restraints weight = 266225.783| |-----------------------------------------------------------------------------| r_work (final): 0.2424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 28632 Z= 0.155 Angle : 0.652 21.420 39087 Z= 0.316 Chirality : 0.044 0.441 4527 Planarity : 0.004 0.134 4944 Dihedral : 7.795 101.512 5067 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3462 helix: 1.56 (0.20), residues: 695 sheet: -0.60 (0.19), residues: 701 loop : -1.04 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.004 0.001 HIS A 264 PHE 0.026 0.001 PHE B 164 TYR 0.019 0.002 TYR C 184 ARG 0.016 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 33) link_NAG-ASN : angle 3.82068 ( 99) link_ALPHA1-6 : bond 0.00833 ( 3) link_ALPHA1-6 : angle 1.49933 ( 9) link_BETA1-4 : bond 0.00747 ( 18) link_BETA1-4 : angle 2.33821 ( 54) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 2.87730 ( 9) hydrogen bonds : bond 0.03381 ( 1021) hydrogen bonds : angle 5.68737 ( 2712) link_BETA1-6 : bond 0.01009 ( 6) link_BETA1-6 : angle 2.81875 ( 18) SS BOND : bond 0.00296 ( 48) SS BOND : angle 1.63648 ( 96) covalent geometry : bond 0.00327 (28521) covalent geometry : angle 0.60876 (38802) *********************** 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 78 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8431 (mmt) cc_final: 0.8220 (mmm) REVERT: A 278 MET cc_start: 0.9420 (tpt) cc_final: 0.8926 (tpp) REVERT: A 296 ILE cc_start: 0.9368 (mp) cc_final: 0.9027 (mp) REVERT: A 686 MET cc_start: 0.8260 (mmp) cc_final: 0.8029 (mmm) REVERT: A 696 MET cc_start: 0.8374 (mmt) cc_final: 0.8035 (mmm) REVERT: A 939 MET cc_start: 0.9565 (tpp) cc_final: 0.9320 (tpp) REVERT: B 148 MET cc_start: 0.9518 (ppp) cc_final: 0.9246 (ppp) REVERT: B 278 MET cc_start: 0.8583 (tpt) cc_final: 0.7718 (tpp) REVERT: B 292 TYR cc_start: 0.9676 (m-80) cc_final: 0.9345 (m-80) REVERT: B 696 MET cc_start: 0.8965 (mmp) cc_final: 0.8479 (mmp) REVERT: B 757 MET cc_start: 0.9074 (mtt) cc_final: 0.8547 (mmp) REVERT: B 906 MET cc_start: 0.9513 (mmp) cc_final: 0.8723 (pmm) REVERT: B 913 MET cc_start: 0.9469 (mtm) cc_final: 0.9196 (mtp) REVERT: B 943 MET cc_start: 0.9132 (mmm) cc_final: 0.8825 (tpt) REVERT: C 757 MET cc_start: 0.9555 (tpt) cc_final: 0.8911 (tpp) REVERT: C 943 MET cc_start: 0.9471 (tpt) cc_final: 0.9191 (tpt) REVERT: C 1137 MET cc_start: 0.9201 (mpp) cc_final: 0.8976 (mpp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3851 time to fit residues: 52.8226 Evaluate side-chains 69 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 108 optimal weight: 20.0000 chunk 301 optimal weight: 30.0000 chunk 3 optimal weight: 4.9990 chunk 245 optimal weight: 40.0000 chunk 127 optimal weight: 40.0000 chunk 202 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 273 optimal weight: 0.0470 chunk 265 optimal weight: 6.9990 overall best weight: 2.7282 ------------------------------------------------------------------------------- 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 ** 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 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** 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 = 0.2799 r_free = 0.2799 target = 0.028102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.021145 restraints weight = 540090.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.021368 restraints weight = 348827.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.021681 restraints weight = 256628.085| |-----------------------------------------------------------------------------| r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3209 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= 0.117 Angle : 0.630 21.135 39087 Z= 0.304 Chirality : 0.044 0.443 4527 Planarity : 0.004 0.104 4944 Dihedral : 7.446 99.367 5067 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3462 helix: 1.60 (0.20), residues: 707 sheet: -0.65 (0.18), residues: 754 loop : -0.96 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 44 HIS 0.005 0.001 HIS B1138 PHE 0.025 0.001 PHE A 467 TYR 0.015 0.001 TYR C 184 ARG 0.014 0.000 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 33) link_NAG-ASN : angle 3.74138 ( 99) link_ALPHA1-6 : bond 0.00937 ( 3) link_ALPHA1-6 : angle 1.55102 ( 9) link_BETA1-4 : bond 0.00767 ( 18) link_BETA1-4 : angle 2.25159 ( 54) link_ALPHA1-3 : bond 0.01254 ( 3) link_ALPHA1-3 : angle 1.99938 ( 9) hydrogen bonds : bond 0.03219 ( 1021) hydrogen bonds : angle 5.50251 ( 2712) link_BETA1-6 : bond 0.01073 ( 6) link_BETA1-6 : angle 2.77986 ( 18) SS BOND : bond 0.00229 ( 48) SS BOND : angle 1.48673 ( 96) covalent geometry : bond 0.00260 (28521) covalent geometry : angle 0.58889 (38802) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 2.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8440 (mmt) cc_final: 0.8232 (mmm) REVERT: A 278 MET cc_start: 0.9405 (tpt) cc_final: 0.8870 (tpp) REVERT: A 296 ILE cc_start: 0.9332 (mp) cc_final: 0.9016 (mp) REVERT: A 686 MET cc_start: 0.8207 (mmp) cc_final: 0.7981 (mmm) REVERT: A 696 MET cc_start: 0.8404 (mmt) cc_final: 0.8023 (mmm) REVERT: A 939 MET cc_start: 0.9564 (tpp) cc_final: 0.9300 (tpp) REVERT: B 148 MET cc_start: 0.9534 (ppp) cc_final: 0.9266 (ppp) REVERT: B 278 MET cc_start: 0.8584 (tpt) cc_final: 0.7790 (tpp) REVERT: B 292 TYR cc_start: 0.9673 (m-80) cc_final: 0.9334 (m-80) REVERT: B 696 MET cc_start: 0.9028 (mmp) cc_final: 0.8547 (mmp) REVERT: B 757 MET cc_start: 0.9116 (mtt) cc_final: 0.8658 (tpp) REVERT: B 906 MET cc_start: 0.9505 (mmp) cc_final: 0.8720 (pmm) REVERT: B 913 MET cc_start: 0.9455 (mtm) cc_final: 0.9132 (mtp) REVERT: B 943 MET cc_start: 0.9057 (mmm) cc_final: 0.8847 (tpt) REVERT: C 563 MET cc_start: 0.9045 (tpt) cc_final: 0.8829 (tpt) REVERT: C 757 MET cc_start: 0.9563 (tpt) cc_final: 0.8927 (tpp) REVERT: C 1137 MET cc_start: 0.9217 (mpp) cc_final: 0.8965 (mpp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3691 time to fit residues: 48.4852 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 : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 290 optimal weight: 20.0000 chunk 213 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 282 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 212 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 76 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 167 HIS A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** 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 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** 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 522 GLN ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.026910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.020042 restraints weight = 555953.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.020219 restraints weight = 368528.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.020506 restraints weight = 274339.569| |-----------------------------------------------------------------------------| r_work (final): 0.2415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28632 Z= 0.193 Angle : 0.674 21.647 39087 Z= 0.332 Chirality : 0.044 0.431 4527 Planarity : 0.004 0.083 4944 Dihedral : 7.338 96.200 5067 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.14), residues: 3462 helix: 1.55 (0.20), residues: 703 sheet: -0.68 (0.19), residues: 709 loop : -0.99 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 310 HIS 0.005 0.001 HIS A 670 PHE 0.031 0.002 PHE B 164 TYR 0.020 0.002 TYR C 184 ARG 0.014 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 33) link_NAG-ASN : angle 3.80817 ( 99) link_ALPHA1-6 : bond 0.00701 ( 3) link_ALPHA1-6 : angle 1.50330 ( 9) link_BETA1-4 : bond 0.00635 ( 18) link_BETA1-4 : angle 2.35934 ( 54) link_ALPHA1-3 : bond 0.00997 ( 3) link_ALPHA1-3 : angle 2.56847 ( 9) hydrogen bonds : bond 0.03552 ( 1021) hydrogen bonds : angle 5.74537 ( 2712) link_BETA1-6 : bond 0.01156 ( 6) link_BETA1-6 : angle 2.73132 ( 18) SS BOND : bond 0.00350 ( 48) SS BOND : angle 1.74404 ( 96) covalent geometry : bond 0.00396 (28521) covalent geometry : angle 0.63240 (38802) ********************** 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 76 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.9386 (tpt) cc_final: 0.8994 (tpp) REVERT: A 296 ILE cc_start: 0.9342 (mp) cc_final: 0.9043 (mp) REVERT: A 686 MET cc_start: 0.8367 (mmp) cc_final: 0.8162 (mmm) REVERT: A 696 MET cc_start: 0.8416 (mmt) cc_final: 0.8161 (mmp) REVERT: A 939 MET cc_start: 0.9587 (tpp) cc_final: 0.9347 (tpp) REVERT: B 278 MET cc_start: 0.8455 (tpt) cc_final: 0.7557 (tpp) REVERT: B 292 TYR cc_start: 0.9687 (m-80) cc_final: 0.9353 (m-80) REVERT: B 696 MET cc_start: 0.8931 (mmp) cc_final: 0.8440 (mmp) REVERT: B 757 MET cc_start: 0.9136 (mtt) cc_final: 0.8688 (mmp) REVERT: B 906 MET cc_start: 0.9547 (mmp) cc_final: 0.8760 (pmm) REVERT: B 913 MET cc_start: 0.9439 (mtm) cc_final: 0.9115 (mtp) REVERT: B 943 MET cc_start: 0.9382 (mmm) cc_final: 0.8862 (tpp) REVERT: C 84 MET cc_start: 0.9525 (mmm) cc_final: 0.9111 (tpp) REVERT: C 757 MET cc_start: 0.9511 (tpt) cc_final: 0.8896 (tpp) REVERT: C 1137 MET cc_start: 0.9198 (mpp) cc_final: 0.8985 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3768 time to fit residues: 50.2683 Evaluate side-chains 68 residues out of total 3009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 90 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 303 optimal weight: 40.0000 chunk 335 optimal weight: 10.0000 chunk 240 optimal weight: 40.0000 chunk 25 optimal weight: 9.9990 chunk 268 optimal weight: 30.0000 chunk 13 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.026443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.019587 restraints weight = 561909.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.019753 restraints weight = 374101.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.020051 restraints weight = 278520.987| |-----------------------------------------------------------------------------| r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28632 Z= 0.215 Angle : 0.703 21.829 39087 Z= 0.347 Chirality : 0.045 0.410 4527 Planarity : 0.005 0.074 4944 Dihedral : 7.397 94.934 5067 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.14), residues: 3462 helix: 1.36 (0.20), residues: 715 sheet: -0.83 (0.19), residues: 679 loop : -1.12 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 310 HIS 0.006 0.001 HIS A 264 PHE 0.031 0.002 PHE B 164 TYR 0.019 0.002 TYR C 184 ARG 0.013 0.001 ARG B 841 Details of bonding type rmsd link_NAG-ASN : bond 0.00666 ( 33) link_NAG-ASN : angle 3.80540 ( 99) link_ALPHA1-6 : bond 0.00688 ( 3) link_ALPHA1-6 : angle 1.51664 ( 9) link_BETA1-4 : bond 0.00655 ( 18) link_BETA1-4 : angle 2.31773 ( 54) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 2.43949 ( 9) hydrogen bonds : bond 0.03687 ( 1021) hydrogen bonds : angle 5.93943 ( 2712) link_BETA1-6 : bond 0.01180 ( 6) link_BETA1-6 : angle 2.70771 ( 18) SS BOND : bond 0.00446 ( 48) SS BOND : angle 1.73914 ( 96) covalent geometry : bond 0.00437 (28521) covalent geometry : angle 0.66347 (38802) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7697.05 seconds wall clock time: 139 minutes 1.81 seconds (8341.81 seconds total)