Starting phenix.real_space_refine on Thu May 29 11:12:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813.map" model { file = "/net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akj_11813/05_2025/7akj_11813_neut.cif" } resolution = 3.8 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= 0.000 sd= 0.002 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 156 5.16 5 C 20211 2.51 5 N 5127 2.21 5 O 6318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "B" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 19.18, per 1000 atoms: 0.60 Number of scatterers: 31812 At special positions: 0 Unit cell: (160.92, 163.08, 183.6, 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 156 16.00 O 6318 8.00 N 5127 7.00 C 20211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.05 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-2 " MAN N 6 " - " MAN N 7 " " MAN T 6 " - " MAN T 7 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " MAN N 6 " - " MAN N 8 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " MAN T 6 " - " MAN T 8 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 8 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA T 3 " - " MAN T 6 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 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 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 9 " " NAG Q 1 " - " FUC Q 3 " " NAG T 1 " - " FUC T 9 " " NAG W 1 " - " FUC W 3 " " NAG Z 1 " - " FUC Z 9 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 318 " " NAG A1305 " - " ASN A 357 " " NAG A1308 " - " ASN A 691 " " NAG A1309 " - " ASN A 699 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A1080 " " NAG A1312 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1303 " - " ASN B 158 " " NAG B1304 " - " ASN B 318 " " NAG B1305 " - " ASN B 357 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 699 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B1080 " " NAG B1312 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1303 " - " ASN C 158 " " NAG C1304 " - " ASN C 318 " " NAG C1305 " - " ASN C 357 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C1080 " " NAG C1312 " - " ASN C1116 " " NAG I 1 " - " ASN C 109 " " NAG J 1 " - " ASN C 119 " " NAG K 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 269 " " NAG N 1 " - " ASN C 330 " " NAG O 1 " - " ASN C 783 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 227 " " NAG S 1 " - " ASN B 269 " " NAG T 1 " - " ASN B 330 " " NAG U 1 " - " ASN B 783 " " NAG V 1 " - " ASN A 109 " " NAG W 1 " - " ASN A 119 " " NAG X 1 " - " ASN A 227 " " NAG Y 1 " - " ASN A 269 " " NAG Z 1 " - " ASN A 330 " " NAG a 1 " - " ASN A 783 " Time building additional restraints: 8.62 Conformation dependent library (CDL) restraints added in 4.1 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 66 sheets defined 22.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.611A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.850A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.794A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.831A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY C 871 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 895 through 901' Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.806A pdb=" N ILE C 905 " --> pdb=" O ASN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.570A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1107 through 1111 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.613A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR B 723 " --> pdb=" O ASP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.524A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 removed outlier: 4.028A pdb=" N ALA B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 901' Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE B 905 " --> pdb=" O ASN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.812A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.714A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.612A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 886 " --> pdb=" O MET A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.327A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 901' Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU C 184 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ASN C 135 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR C 150 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE C 137 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR C 148 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 113 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 117 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 124 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 302 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 422 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 363 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 441 removed outlier: 6.155A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C1029 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1076 through 1079 Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.581A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 152 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR B 150 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE B 137 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR B 148 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 117 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 124 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 302 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.745A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 422 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 363 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR B 436 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE B 483 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 438 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1029 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.990A pdb=" N CYS G 95 " --> pdb=" O TRP G 111 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP G 111 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG G 97 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS E 95 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP E 111 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG E 97 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.501A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 184 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE A 137 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR A 148 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 236 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 98 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 117 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.679A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 422 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 363 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AF8, first strand: chain 'A' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR A 436 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 483 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.721A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.268A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.700A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA A1037 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A1029 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AG4, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AG5, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 2988 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: 16.57 Time building geometry restraints manager: 9.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9939 1.35 - 1.48: 8879 1.48 - 1.61: 13525 1.61 - 1.73: 3 1.73 - 1.86: 210 Bond restraints: 32556 Sorted by residual: bond pdb=" C1 MAN N 5 " pdb=" C2 MAN N 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN Z 5 " pdb=" C2 MAN Z 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN T 5 " pdb=" C2 MAN T 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 32551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 43029 2.35 - 4.70: 1110 4.70 - 7.04: 148 7.04 - 9.39: 26 9.39 - 11.74: 12 Bond angle restraints: 44325 Sorted by residual: angle pdb=" CA CYS B 635 " pdb=" CB CYS B 635 " pdb=" SG CYS B 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS A 635 " pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS C 635 " pdb=" CB CYS C 635 " pdb=" SG CYS C 635 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" CA CYS B 720 " pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " ideal model delta sigma weight residual 114.40 125.27 -10.87 2.30e+00 1.89e-01 2.23e+01 angle pdb=" CA CYS A 720 " pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " ideal model delta sigma weight residual 114.40 125.25 -10.85 2.30e+00 1.89e-01 2.23e+01 ... (remaining 44320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 19434 23.51 - 47.03: 702 47.03 - 70.54: 219 70.54 - 94.05: 123 94.05 - 117.56: 66 Dihedral angle restraints: 20544 sinusoidal: 9135 harmonic: 11409 Sorted by residual: dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.50 -88.50 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 20541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 5226 0.215 - 0.430: 27 0.430 - 0.644: 6 0.644 - 0.859: 3 0.859 - 1.074: 3 Chirality restraints: 5265 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 119 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 119 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 119 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.86e+01 ... (remaining 5262 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 119 " -0.047 2.00e-02 2.50e+03 4.73e-02 2.79e+01 pdb=" CG ASN B 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 119 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 119 " -0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN A 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 119 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 119 " 0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN C 119 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 119 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 119 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.054 2.00e-02 2.50e+03 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 852 2.69 - 3.25: 30936 3.25 - 3.80: 43714 3.80 - 4.35: 57195 4.35 - 4.90: 97605 Nonbonded interactions: 230302 Sorted by model distance: nonbonded pdb=" OG1 THR C 693 " pdb=" OE1 GLN A 877 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLN B 877 " pdb=" OG1 THR A 693 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLN C 877 " pdb=" OG1 THR B 693 " model vdw 2.153 3.040 nonbonded pdb=" O2 MAN T 4 " pdb=" O5 MAN T 5 " model vdw 2.161 3.040 nonbonded pdb=" O2 MAN Z 4 " pdb=" O5 MAN Z 5 " model vdw 2.162 3.040 ... (remaining 230297 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.320 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 76.940 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 0.103 32694 Z= 0.244 Angle : 1.043 22.392 44688 Z= 0.503 Chirality : 0.068 1.074 5265 Planarity : 0.005 0.080 5577 Dihedral : 16.704 117.563 13071 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -1.03 (0.12), residues: 3888 helix: -1.38 (0.18), residues: 657 sheet: 0.66 (0.16), residues: 939 loop : -1.06 (0.11), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 245 HIS 0.006 0.001 HIS C1030 PHE 0.045 0.002 PHE A 130 TYR 0.027 0.002 TYR H 52 ARG 0.023 0.003 ARG B 232 Details of bonding type rmsd link_NAG-ASN : bond 0.01267 ( 45) link_NAG-ASN : angle 9.15909 ( 135) link_ALPHA1-6 : bond 0.01350 ( 3) link_ALPHA1-6 : angle 1.20922 ( 9) link_BETA1-4 : bond 0.00443 ( 21) link_BETA1-4 : angle 2.32040 ( 63) link_ALPHA1-2 : bond 0.01085 ( 3) link_ALPHA1-2 : angle 0.76379 ( 9) link_ALPHA1-3 : bond 0.02379 ( 9) link_ALPHA1-3 : angle 5.66933 ( 27) hydrogen bonds : bond 0.23656 ( 1092) hydrogen bonds : angle 8.39559 ( 2988) link_BETA1-6 : bond 0.01225 ( 6) link_BETA1-6 : angle 1.30354 ( 18) SS BOND : bond 0.00635 ( 51) SS BOND : angle 3.22657 ( 102) covalent geometry : bond 0.00519 (32556) covalent geometry : angle 0.88883 (44325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 305 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.6983 (mmt) cc_final: 0.6129 (mmt) REVERT: G 52 TYR cc_start: 0.8014 (p90) cc_final: 0.7796 (p90) REVERT: A 151 MET cc_start: 0.6931 (mmt) cc_final: 0.6274 (mmt) REVERT: H 14 PRO cc_start: 0.2936 (Cg_endo) cc_final: 0.2350 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.3915 time to fit residues: 201.3823 Evaluate side-chains 212 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 157 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 354 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN B 409 ASN G 58 ASN E 58 ASN A 939 GLN H 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.106122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085669 restraints weight = 70234.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085430 restraints weight = 66385.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.086304 restraints weight = 64953.104| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32694 Z= 0.177 Angle : 0.900 18.730 44688 Z= 0.417 Chirality : 0.055 0.523 5265 Planarity : 0.005 0.054 5577 Dihedral : 13.103 82.878 6177 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.06 % Allowed : 4.89 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.21 (0.13), residues: 3888 helix: 0.47 (0.20), residues: 654 sheet: 1.22 (0.18), residues: 828 loop : -0.84 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 245 HIS 0.005 0.001 HIS C1030 PHE 0.019 0.002 PHE C 483 TYR 0.023 0.002 TYR C1049 ARG 0.008 0.001 ARG A 747 Details of bonding type rmsd link_NAG-ASN : bond 0.01068 ( 45) link_NAG-ASN : angle 7.17106 ( 135) link_ALPHA1-6 : bond 0.00248 ( 3) link_ALPHA1-6 : angle 1.59048 ( 9) link_BETA1-4 : bond 0.00613 ( 21) link_BETA1-4 : angle 1.97589 ( 63) link_ALPHA1-2 : bond 0.01464 ( 3) link_ALPHA1-2 : angle 2.71792 ( 9) link_ALPHA1-3 : bond 0.02822 ( 9) link_ALPHA1-3 : angle 6.27023 ( 27) hydrogen bonds : bond 0.06449 ( 1092) hydrogen bonds : angle 6.01013 ( 2988) link_BETA1-6 : bond 0.01009 ( 6) link_BETA1-6 : angle 1.19555 ( 18) SS BOND : bond 0.00484 ( 51) SS BOND : angle 2.53558 ( 102) covalent geometry : bond 0.00386 (32556) covalent geometry : angle 0.78247 (44325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7963 (mpp) cc_final: 0.7562 (mpp) REVERT: C 151 MET cc_start: 0.7242 (mmt) cc_final: 0.6956 (mmt) REVERT: B 130 PHE cc_start: 0.5793 (m-10) cc_final: 0.5436 (m-10) REVERT: B 151 MET cc_start: 0.7171 (mmt) cc_final: 0.6281 (mmt) REVERT: G 52 TYR cc_start: 0.8023 (p90) cc_final: 0.7734 (p90) REVERT: A 144 MET cc_start: 0.8058 (mpp) cc_final: 0.7309 (mpp) outliers start: 36 outliers final: 26 residues processed: 263 average time/residue: 0.3770 time to fit residues: 166.1840 Evaluate side-chains 251 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 29 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 253 optimal weight: 6.9990 chunk 187 optimal weight: 0.0020 chunk 27 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 349 optimal weight: 4.9990 chunk 359 optimal weight: 0.8980 overall best weight: 2.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 ASN C 939 GLN ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.081938 restraints weight = 71739.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.081464 restraints weight = 70997.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081922 restraints weight = 91837.904| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 32694 Z= 0.231 Angle : 0.894 17.963 44688 Z= 0.422 Chirality : 0.056 0.526 5265 Planarity : 0.005 0.044 5577 Dihedral : 10.775 63.538 6177 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.03 % Allowed : 7.57 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.46 (0.13), residues: 3888 helix: 0.66 (0.21), residues: 654 sheet: 1.03 (0.18), residues: 858 loop : -1.15 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 102 HIS 0.006 0.001 HIS C1046 PHE 0.021 0.002 PHE A 558 TYR 0.030 0.002 TYR C 481 ARG 0.009 0.001 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00969 ( 45) link_NAG-ASN : angle 6.82270 ( 135) link_ALPHA1-6 : bond 0.00276 ( 3) link_ALPHA1-6 : angle 3.01748 ( 9) link_BETA1-4 : bond 0.00532 ( 21) link_BETA1-4 : angle 1.95670 ( 63) link_ALPHA1-2 : bond 0.01934 ( 3) link_ALPHA1-2 : angle 2.66852 ( 9) link_ALPHA1-3 : bond 0.02620 ( 9) link_ALPHA1-3 : angle 6.48964 ( 27) hydrogen bonds : bond 0.07198 ( 1092) hydrogen bonds : angle 5.79512 ( 2988) link_BETA1-6 : bond 0.01034 ( 6) link_BETA1-6 : angle 1.05261 ( 18) SS BOND : bond 0.00709 ( 51) SS BOND : angle 2.58465 ( 102) covalent geometry : bond 0.00551 (32556) covalent geometry : angle 0.78295 (44325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 PHE cc_start: 0.6364 (m-10) cc_final: 0.6138 (m-10) REVERT: C 144 MET cc_start: 0.8007 (mpp) cc_final: 0.7675 (mpp) REVERT: C 151 MET cc_start: 0.7341 (mmt) cc_final: 0.7095 (mmt) REVERT: C 1045 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8352 (pp) REVERT: B 130 PHE cc_start: 0.6336 (m-10) cc_final: 0.5929 (m-10) REVERT: B 151 MET cc_start: 0.7434 (mmt) cc_final: 0.6637 (mmt) REVERT: B 1045 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8382 (pp) REVERT: G 38 ARG cc_start: 0.7510 (ptt-90) cc_final: 0.7257 (ptt-90) REVERT: E 50 TYR cc_start: 0.8251 (p90) cc_final: 0.8036 (p90) REVERT: D 18 ARG cc_start: 0.6542 (ptm160) cc_final: 0.6333 (ptm160) REVERT: A 708 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (m) outliers start: 69 outliers final: 39 residues processed: 277 average time/residue: 0.3790 time to fit residues: 176.5263 Evaluate side-chains 255 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 105 GLU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 219 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 191 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 348 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 356 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 756 GLN ** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 939 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.103252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.082986 restraints weight = 71393.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.083129 restraints weight = 71264.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083680 restraints weight = 80244.102| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32694 Z= 0.170 Angle : 0.820 17.226 44688 Z= 0.379 Chirality : 0.054 0.521 5265 Planarity : 0.004 0.040 5577 Dihedral : 10.168 59.992 6177 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.21 % Allowed : 9.28 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.38 (0.13), residues: 3888 helix: 0.93 (0.21), residues: 654 sheet: 1.18 (0.18), residues: 843 loop : -1.20 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 423 HIS 0.004 0.001 HIS B1030 PHE 0.020 0.002 PHE B 483 TYR 0.019 0.002 TYR C1049 ARG 0.004 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00901 ( 45) link_NAG-ASN : angle 6.47909 ( 135) link_ALPHA1-6 : bond 0.00611 ( 3) link_ALPHA1-6 : angle 2.69977 ( 9) link_BETA1-4 : bond 0.00446 ( 21) link_BETA1-4 : angle 1.89270 ( 63) link_ALPHA1-2 : bond 0.01993 ( 3) link_ALPHA1-2 : angle 2.60704 ( 9) link_ALPHA1-3 : bond 0.02592 ( 9) link_ALPHA1-3 : angle 6.26967 ( 27) hydrogen bonds : bond 0.06058 ( 1092) hydrogen bonds : angle 5.52138 ( 2988) link_BETA1-6 : bond 0.00903 ( 6) link_BETA1-6 : angle 1.07664 ( 18) SS BOND : bond 0.00440 ( 51) SS BOND : angle 2.12136 ( 102) covalent geometry : bond 0.00386 (32556) covalent geometry : angle 0.71223 (44325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 PHE cc_start: 0.6311 (m-10) cc_final: 0.6104 (m-10) REVERT: C 144 MET cc_start: 0.7955 (mpp) cc_final: 0.7655 (mpp) REVERT: C 151 MET cc_start: 0.7285 (mmt) cc_final: 0.7063 (mmt) REVERT: C 770 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7213 (mtm) REVERT: C 884 MET cc_start: 0.8839 (mmp) cc_final: 0.8226 (mmt) REVERT: C 1045 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 130 PHE cc_start: 0.6349 (m-10) cc_final: 0.6031 (m-10) REVERT: B 144 MET cc_start: 0.7837 (mpp) cc_final: 0.7145 (mpp) REVERT: B 151 MET cc_start: 0.7525 (mmt) cc_final: 0.6735 (mmt) REVERT: B 295 ILE cc_start: 0.8670 (mp) cc_final: 0.8387 (mm) REVERT: B 1045 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8317 (pp) REVERT: E 38 ARG cc_start: 0.7450 (ptt180) cc_final: 0.6962 (ptt-90) REVERT: E 50 TYR cc_start: 0.8276 (p90) cc_final: 0.7968 (p90) REVERT: A 144 MET cc_start: 0.7968 (mpp) cc_final: 0.7357 (mpp) outliers start: 75 outliers final: 47 residues processed: 277 average time/residue: 0.3845 time to fit residues: 178.5457 Evaluate side-chains 261 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 83 optimal weight: 0.0980 chunk 348 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 253 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS C 409 ASN B 70 HIS A 70 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082221 restraints weight = 71313.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.081381 restraints weight = 72888.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082274 restraints weight = 75493.989| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32694 Z= 0.185 Angle : 0.815 17.171 44688 Z= 0.380 Chirality : 0.054 0.527 5265 Planarity : 0.005 0.039 5577 Dihedral : 9.621 59.695 6177 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.94 % Allowed : 9.72 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.53 (0.13), residues: 3888 helix: 0.92 (0.21), residues: 654 sheet: 1.02 (0.18), residues: 840 loop : -1.31 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 245 HIS 0.004 0.001 HIS C1046 PHE 0.016 0.002 PHE A 89 TYR 0.021 0.002 TYR C1049 ARG 0.005 0.000 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00871 ( 45) link_NAG-ASN : angle 6.09772 ( 135) link_ALPHA1-6 : bond 0.00588 ( 3) link_ALPHA1-6 : angle 2.21802 ( 9) link_BETA1-4 : bond 0.00452 ( 21) link_BETA1-4 : angle 1.88644 ( 63) link_ALPHA1-2 : bond 0.02127 ( 3) link_ALPHA1-2 : angle 2.31080 ( 9) link_ALPHA1-3 : bond 0.02529 ( 9) link_ALPHA1-3 : angle 6.35259 ( 27) hydrogen bonds : bond 0.06201 ( 1092) hydrogen bonds : angle 5.45613 ( 2988) link_BETA1-6 : bond 0.00939 ( 6) link_BETA1-6 : angle 1.09540 ( 18) SS BOND : bond 0.00473 ( 51) SS BOND : angle 2.13289 ( 102) covalent geometry : bond 0.00432 (32556) covalent geometry : angle 0.71635 (44325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 223 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7910 (mpp) cc_final: 0.7629 (mpp) REVERT: C 151 MET cc_start: 0.7238 (mmt) cc_final: 0.6980 (mmt) REVERT: C 770 MET cc_start: 0.7787 (OUTLIER) cc_final: 0.7146 (mtm) REVERT: C 884 MET cc_start: 0.8755 (mmp) cc_final: 0.8242 (mmt) REVERT: C 1045 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8377 (pp) REVERT: B 130 PHE cc_start: 0.6382 (m-10) cc_final: 0.6114 (m-10) REVERT: B 144 MET cc_start: 0.7844 (mpp) cc_final: 0.7194 (mpp) REVERT: B 151 MET cc_start: 0.7464 (mmt) cc_final: 0.6719 (mmt) REVERT: B 295 ILE cc_start: 0.8711 (mp) cc_final: 0.8428 (mm) REVERT: B 1045 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8397 (pp) REVERT: G 64 LYS cc_start: 0.6534 (OUTLIER) cc_final: 0.5739 (pttp) REVERT: E 38 ARG cc_start: 0.7490 (ptt180) cc_final: 0.7137 (ptt-90) REVERT: E 50 TYR cc_start: 0.8253 (p90) cc_final: 0.7930 (p90) REVERT: E 64 LYS cc_start: 0.6578 (OUTLIER) cc_final: 0.5592 (pttp) REVERT: E 100 LEU cc_start: 0.9174 (tp) cc_final: 0.8915 (tt) REVERT: A 144 MET cc_start: 0.7907 (mpp) cc_final: 0.7375 (mpp) REVERT: H 64 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.5591 (pttp) outliers start: 100 outliers final: 63 residues processed: 295 average time/residue: 0.4043 time to fit residues: 197.9360 Evaluate side-chains 278 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 352 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 308 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.104012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.083992 restraints weight = 70900.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083199 restraints weight = 71448.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084232 restraints weight = 79037.720| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 32694 Z= 0.140 Angle : 0.766 16.370 44688 Z= 0.353 Chirality : 0.053 0.502 5265 Planarity : 0.004 0.041 5577 Dihedral : 9.068 59.922 6177 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 10.87 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.38 (0.13), residues: 3888 helix: 1.09 (0.21), residues: 657 sheet: 1.07 (0.18), residues: 840 loop : -1.20 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 245 HIS 0.004 0.001 HIS B1030 PHE 0.017 0.001 PHE C 130 TYR 0.030 0.001 TYR C 481 ARG 0.003 0.000 ARG C 747 Details of bonding type rmsd link_NAG-ASN : bond 0.00843 ( 45) link_NAG-ASN : angle 5.87897 ( 135) link_ALPHA1-6 : bond 0.00223 ( 3) link_ALPHA1-6 : angle 1.92372 ( 9) link_BETA1-4 : bond 0.00446 ( 21) link_BETA1-4 : angle 1.82613 ( 63) link_ALPHA1-2 : bond 0.02272 ( 3) link_ALPHA1-2 : angle 1.81018 ( 9) link_ALPHA1-3 : bond 0.02513 ( 9) link_ALPHA1-3 : angle 6.30933 ( 27) hydrogen bonds : bond 0.05325 ( 1092) hydrogen bonds : angle 5.23917 ( 2988) link_BETA1-6 : bond 0.00853 ( 6) link_BETA1-6 : angle 1.14231 ( 18) SS BOND : bond 0.00366 ( 51) SS BOND : angle 2.20641 ( 102) covalent geometry : bond 0.00301 (32556) covalent geometry : angle 0.66654 (44325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 234 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7950 (mpp) cc_final: 0.7726 (mpp) REVERT: C 151 MET cc_start: 0.7169 (mmt) cc_final: 0.6968 (mmt) REVERT: C 770 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7062 (mtm) REVERT: C 884 MET cc_start: 0.8647 (mmp) cc_final: 0.8213 (mmt) REVERT: C 1045 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 130 PHE cc_start: 0.6304 (m-10) cc_final: 0.6042 (m-10) REVERT: B 144 MET cc_start: 0.7924 (mpp) cc_final: 0.7219 (mpp) REVERT: B 151 MET cc_start: 0.7451 (mmt) cc_final: 0.6904 (mmt) REVERT: B 295 ILE cc_start: 0.8581 (mp) cc_final: 0.8279 (mm) REVERT: B 770 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7506 (mtm) REVERT: B 1045 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 38 ARG cc_start: 0.7405 (ptt180) cc_final: 0.7074 (ptt-90) REVERT: E 50 TYR cc_start: 0.8193 (p90) cc_final: 0.7966 (p90) REVERT: E 64 LYS cc_start: 0.6589 (OUTLIER) cc_final: 0.5612 (pttp) REVERT: A 144 MET cc_start: 0.7895 (mpp) cc_final: 0.7479 (mpp) REVERT: H 50 TYR cc_start: 0.7896 (p90) cc_final: 0.7594 (p90) REVERT: H 64 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5555 (pttp) outliers start: 73 outliers final: 44 residues processed: 282 average time/residue: 0.3965 time to fit residues: 185.2997 Evaluate side-chains 260 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 288 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 299 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 276 optimal weight: 0.7980 chunk 287 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 389 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 77 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084642 restraints weight = 70573.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083996 restraints weight = 71003.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084806 restraints weight = 74972.101| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32694 Z= 0.128 Angle : 0.740 16.226 44688 Z= 0.340 Chirality : 0.052 0.506 5265 Planarity : 0.004 0.042 5577 Dihedral : 8.628 59.912 6177 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.12 % Allowed : 11.87 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.29 (0.13), residues: 3888 helix: 1.15 (0.21), residues: 666 sheet: 1.03 (0.18), residues: 858 loop : -1.12 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 245 HIS 0.004 0.001 HIS C1030 PHE 0.015 0.001 PHE C 22 TYR 0.032 0.001 TYR C 481 ARG 0.003 0.000 ARG A 747 Details of bonding type rmsd link_NAG-ASN : bond 0.00847 ( 45) link_NAG-ASN : angle 5.55900 ( 135) link_ALPHA1-6 : bond 0.00094 ( 3) link_ALPHA1-6 : angle 1.59814 ( 9) link_BETA1-4 : bond 0.00437 ( 21) link_BETA1-4 : angle 1.78674 ( 63) link_ALPHA1-2 : bond 0.02169 ( 3) link_ALPHA1-2 : angle 1.65484 ( 9) link_ALPHA1-3 : bond 0.02542 ( 9) link_ALPHA1-3 : angle 6.32568 ( 27) hydrogen bonds : bond 0.04968 ( 1092) hydrogen bonds : angle 5.08279 ( 2988) link_BETA1-6 : bond 0.00817 ( 6) link_BETA1-6 : angle 1.16933 ( 18) SS BOND : bond 0.00365 ( 51) SS BOND : angle 1.75157 ( 102) covalent geometry : bond 0.00267 (32556) covalent geometry : angle 0.64893 (44325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 229 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7878 (mpp) cc_final: 0.7601 (mpp) REVERT: C 884 MET cc_start: 0.8496 (mmp) cc_final: 0.8162 (mmt) REVERT: C 1045 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8346 (pp) REVERT: B 130 PHE cc_start: 0.6217 (m-10) cc_final: 0.6003 (m-10) REVERT: B 144 MET cc_start: 0.7902 (mpp) cc_final: 0.7205 (mpp) REVERT: B 151 MET cc_start: 0.7414 (mmt) cc_final: 0.7054 (mmt) REVERT: B 295 ILE cc_start: 0.8550 (mp) cc_final: 0.8280 (mm) REVERT: B 770 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7546 (mtm) REVERT: B 1045 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8184 (pp) REVERT: G 64 LYS cc_start: 0.6608 (OUTLIER) cc_final: 0.5844 (pttp) REVERT: E 38 ARG cc_start: 0.7401 (ptt180) cc_final: 0.7076 (ptt-90) REVERT: E 50 TYR cc_start: 0.8170 (p90) cc_final: 0.7915 (p90) REVERT: E 64 LYS cc_start: 0.6540 (OUTLIER) cc_final: 0.5577 (pttp) REVERT: A 144 MET cc_start: 0.7856 (mpp) cc_final: 0.7503 (mpp) REVERT: H 50 TYR cc_start: 0.7916 (p90) cc_final: 0.7582 (p90) REVERT: H 64 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5590 (pttp) outliers start: 72 outliers final: 51 residues processed: 274 average time/residue: 0.4002 time to fit residues: 182.5337 Evaluate side-chains 270 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 264 optimal weight: 3.9990 chunk 362 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.100624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080543 restraints weight = 71395.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.079904 restraints weight = 74376.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.080831 restraints weight = 82490.143| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 32694 Z= 0.256 Angle : 0.876 16.368 44688 Z= 0.417 Chirality : 0.057 0.512 5265 Planarity : 0.005 0.038 5577 Dihedral : 9.073 59.922 6177 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.47 % Allowed : 12.04 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.84 (0.13), residues: 3888 helix: 0.93 (0.21), residues: 639 sheet: 0.67 (0.18), residues: 867 loop : -1.55 (0.11), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 245 HIS 0.006 0.001 HIS C1046 PHE 0.029 0.002 PHE A 741 TYR 0.033 0.002 TYR C 481 ARG 0.011 0.001 ARG C 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00836 ( 45) link_NAG-ASN : angle 5.89832 ( 135) link_ALPHA1-6 : bond 0.00112 ( 3) link_ALPHA1-6 : angle 2.10989 ( 9) link_BETA1-4 : bond 0.00489 ( 21) link_BETA1-4 : angle 1.86871 ( 63) link_ALPHA1-2 : bond 0.01855 ( 3) link_ALPHA1-2 : angle 1.71098 ( 9) link_ALPHA1-3 : bond 0.02268 ( 9) link_ALPHA1-3 : angle 6.50572 ( 27) hydrogen bonds : bond 0.06947 ( 1092) hydrogen bonds : angle 5.56214 ( 2988) link_BETA1-6 : bond 0.00938 ( 6) link_BETA1-6 : angle 1.17252 ( 18) SS BOND : bond 0.00647 ( 51) SS BOND : angle 2.46474 ( 102) covalent geometry : bond 0.00623 (32556) covalent geometry : angle 0.78777 (44325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 224 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7919 (mpp) cc_final: 0.7371 (mpp) REVERT: C 770 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: C 1045 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8432 (pp) REVERT: B 130 PHE cc_start: 0.6695 (m-10) cc_final: 0.6397 (m-10) REVERT: B 144 MET cc_start: 0.7976 (mpp) cc_final: 0.7215 (mpp) REVERT: B 151 MET cc_start: 0.7451 (mmt) cc_final: 0.6966 (mmt) REVERT: B 295 ILE cc_start: 0.8670 (mp) cc_final: 0.8415 (mm) REVERT: B 770 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7449 (mtm) REVERT: B 1045 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8473 (pp) REVERT: G 64 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5663 (pttp) REVERT: G 77 GLN cc_start: 0.8295 (mt0) cc_final: 0.8046 (mt0) REVERT: E 38 ARG cc_start: 0.7553 (ptt180) cc_final: 0.7231 (ptt-90) REVERT: E 64 LYS cc_start: 0.6385 (OUTLIER) cc_final: 0.5322 (pttp) REVERT: A 144 MET cc_start: 0.7909 (mpp) cc_final: 0.7696 (mpp) REVERT: A 741 PHE cc_start: 0.7253 (p90) cc_final: 0.6877 (p90) REVERT: H 50 TYR cc_start: 0.7963 (p90) cc_final: 0.7517 (p90) REVERT: H 64 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5598 (pttp) outliers start: 84 outliers final: 70 residues processed: 283 average time/residue: 0.3936 time to fit residues: 184.6842 Evaluate side-chains 291 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 214 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1014 CYS Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1086 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1014 CYS Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1086 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 63 optimal weight: 0.6980 chunk 161 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 280 optimal weight: 0.1980 chunk 221 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 262 optimal weight: 0.6980 chunk 148 optimal weight: 8.9990 chunk 119 optimal weight: 5.9990 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.104356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084250 restraints weight = 70497.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083470 restraints weight = 70144.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084706 restraints weight = 66420.989| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32694 Z= 0.126 Angle : 0.739 16.169 44688 Z= 0.340 Chirality : 0.051 0.504 5265 Planarity : 0.004 0.041 5577 Dihedral : 8.426 59.994 6177 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.52 (0.13), residues: 3888 helix: 1.13 (0.21), residues: 660 sheet: 0.91 (0.18), residues: 861 loop : -1.34 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 94 HIS 0.004 0.001 HIS C1030 PHE 0.017 0.001 PHE A 483 TYR 0.031 0.001 TYR C 481 ARG 0.006 0.000 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00809 ( 45) link_NAG-ASN : angle 5.37153 ( 135) link_ALPHA1-6 : bond 0.00284 ( 3) link_ALPHA1-6 : angle 1.33118 ( 9) link_BETA1-4 : bond 0.00449 ( 21) link_BETA1-4 : angle 1.77028 ( 63) link_ALPHA1-2 : bond 0.01804 ( 3) link_ALPHA1-2 : angle 2.17372 ( 9) link_ALPHA1-3 : bond 0.02469 ( 9) link_ALPHA1-3 : angle 6.30877 ( 27) hydrogen bonds : bond 0.04917 ( 1092) hydrogen bonds : angle 5.11708 ( 2988) link_BETA1-6 : bond 0.00718 ( 6) link_BETA1-6 : angle 1.23826 ( 18) SS BOND : bond 0.00361 ( 51) SS BOND : angle 1.61988 ( 102) covalent geometry : bond 0.00259 (32556) covalent geometry : angle 0.65245 (44325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 229 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7854 (mpp) cc_final: 0.7593 (mpp) REVERT: C 770 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7127 (mtm) REVERT: C 1045 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8346 (pp) REVERT: B 130 PHE cc_start: 0.6299 (m-10) cc_final: 0.6098 (m-10) REVERT: B 144 MET cc_start: 0.7879 (mpp) cc_final: 0.7153 (mpp) REVERT: B 770 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7478 (mtm) REVERT: B 884 MET cc_start: 0.8752 (mmp) cc_final: 0.8372 (tpt) REVERT: B 1045 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8178 (pp) REVERT: G 64 LYS cc_start: 0.6628 (OUTLIER) cc_final: 0.5855 (pttp) REVERT: E 38 ARG cc_start: 0.7435 (ptt180) cc_final: 0.7131 (ptt-90) REVERT: E 64 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.5432 (pttp) REVERT: A 245 TRP cc_start: 0.7397 (p-90) cc_final: 0.7117 (p-90) REVERT: A 648 CYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6279 (m) REVERT: A 741 PHE cc_start: 0.6665 (p90) cc_final: 0.6252 (t80) REVERT: H 50 TYR cc_start: 0.7880 (p90) cc_final: 0.7587 (p90) REVERT: H 64 LYS cc_start: 0.6338 (OUTLIER) cc_final: 0.5634 (pttp) outliers start: 63 outliers final: 45 residues processed: 276 average time/residue: 0.4068 time to fit residues: 184.0416 Evaluate side-chains 274 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 221 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 179 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 146 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.101241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.080707 restraints weight = 71525.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080070 restraints weight = 74847.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.080805 restraints weight = 91616.851| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 32694 Z= 0.232 Angle : 0.835 16.008 44688 Z= 0.394 Chirality : 0.055 0.503 5265 Planarity : 0.005 0.043 5577 Dihedral : 8.736 59.934 6177 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.88 % Allowed : 12.99 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.77 (0.13), residues: 3888 helix: 1.11 (0.21), residues: 639 sheet: 0.69 (0.18), residues: 867 loop : -1.53 (0.11), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 245 HIS 0.005 0.001 HIS C1046 PHE 0.021 0.002 PHE A 89 TYR 0.035 0.002 TYR C 481 ARG 0.006 0.001 ARG A1021 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 45) link_NAG-ASN : angle 5.63894 ( 135) link_ALPHA1-6 : bond 0.00064 ( 3) link_ALPHA1-6 : angle 1.70890 ( 9) link_BETA1-4 : bond 0.00442 ( 21) link_BETA1-4 : angle 1.79549 ( 63) link_ALPHA1-2 : bond 0.01431 ( 3) link_ALPHA1-2 : angle 2.18916 ( 9) link_ALPHA1-3 : bond 0.02154 ( 9) link_ALPHA1-3 : angle 6.43418 ( 27) hydrogen bonds : bond 0.06382 ( 1092) hydrogen bonds : angle 5.38501 ( 2988) link_BETA1-6 : bond 0.00889 ( 6) link_BETA1-6 : angle 1.20509 ( 18) SS BOND : bond 0.00620 ( 51) SS BOND : angle 2.27594 ( 102) covalent geometry : bond 0.00565 (32556) covalent geometry : angle 0.74965 (44325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 218 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7922 (mpp) cc_final: 0.7377 (mpp) REVERT: C 770 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7292 (mtm) REVERT: C 1045 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8408 (pp) REVERT: B 130 PHE cc_start: 0.6553 (m-10) cc_final: 0.6321 (m-10) REVERT: B 144 MET cc_start: 0.7993 (mpp) cc_final: 0.7292 (mpp) REVERT: B 151 MET cc_start: 0.7624 (mmt) cc_final: 0.7278 (mmt) REVERT: B 295 ILE cc_start: 0.8628 (mp) cc_final: 0.8352 (mm) REVERT: B 770 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: B 1032 MET cc_start: 0.8010 (mtm) cc_final: 0.7798 (mtm) REVERT: B 1045 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8432 (pp) REVERT: G 64 LYS cc_start: 0.6467 (OUTLIER) cc_final: 0.5674 (pttp) REVERT: E 36 TRP cc_start: 0.8165 (m100) cc_final: 0.7485 (m100) REVERT: E 38 ARG cc_start: 0.7516 (ptt180) cc_final: 0.7240 (ptt-90) REVERT: E 64 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.5386 (pttp) REVERT: A 245 TRP cc_start: 0.7416 (p-90) cc_final: 0.7105 (p-90) REVERT: H 50 TYR cc_start: 0.7953 (p90) cc_final: 0.7586 (p90) REVERT: H 64 LYS cc_start: 0.6350 (OUTLIER) cc_final: 0.5535 (pttp) outliers start: 64 outliers final: 52 residues processed: 263 average time/residue: 0.4014 time to fit residues: 175.0056 Evaluate side-chains 275 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 556 SER Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 770 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 888 PHE Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1014 CYS Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.924 > 50: distance: 12 - 137: 23.979 distance: 15 - 134: 12.935 distance: 22 - 133: 13.466 distance: 56 - 65: 13.993 distance: 65 - 66: 16.778 distance: 66 - 67: 16.292 distance: 66 - 69: 3.562 distance: 67 - 68: 17.600 distance: 67 - 74: 19.637 distance: 69 - 70: 11.757 distance: 70 - 71: 8.978 distance: 71 - 72: 18.552 distance: 72 - 73: 9.305 distance: 74 - 75: 13.984 distance: 75 - 76: 15.879 distance: 75 - 78: 17.876 distance: 76 - 77: 23.580 distance: 76 - 82: 18.875 distance: 78 - 79: 25.940 distance: 79 - 80: 24.368 distance: 79 - 81: 12.472 distance: 82 - 83: 22.532 distance: 82 - 88: 17.878 distance: 83 - 84: 31.798 distance: 83 - 86: 35.770 distance: 84 - 85: 8.080 distance: 84 - 89: 41.839 distance: 86 - 87: 41.524 distance: 87 - 88: 27.869 distance: 89 - 90: 20.843 distance: 90 - 91: 21.490 distance: 90 - 93: 5.600 distance: 91 - 92: 15.646 distance: 91 - 97: 20.896 distance: 93 - 94: 23.535 distance: 94 - 95: 13.635 distance: 94 - 96: 5.960 distance: 97 - 98: 13.720 distance: 98 - 99: 19.619 distance: 98 - 101: 16.356 distance: 99 - 100: 9.563 distance: 99 - 105: 42.412 distance: 101 - 102: 22.071 distance: 102 - 103: 28.426 distance: 102 - 104: 16.094 distance: 105 - 106: 12.656 distance: 106 - 107: 38.219 distance: 106 - 109: 23.969 distance: 107 - 108: 14.398 distance: 107 - 116: 23.150 distance: 109 - 110: 15.412 distance: 110 - 111: 38.704 distance: 110 - 112: 18.143 distance: 111 - 113: 5.338 distance: 112 - 114: 12.599 distance: 113 - 115: 42.447 distance: 114 - 115: 38.905 distance: 116 - 117: 13.092 distance: 117 - 118: 26.653 distance: 117 - 120: 23.998 distance: 118 - 119: 4.499 distance: 118 - 124: 22.949 distance: 120 - 121: 30.436 distance: 121 - 122: 25.919 distance: 122 - 123: 9.097 distance: 124 - 125: 6.167 distance: 125 - 126: 31.007 distance: 126 - 127: 42.061 distance: 126 - 128: 16.672 distance: 128 - 129: 12.811 distance: 128 - 183: 10.197 distance: 129 - 130: 10.704 distance: 129 - 132: 24.230 distance: 130 - 131: 31.247 distance: 130 - 134: 11.190 distance: 131 - 180: 36.175 distance: 132 - 133: 24.947 distance: 134 - 135: 16.386 distance: 135 - 136: 31.510 distance: 135 - 138: 9.382 distance: 136 - 137: 41.721 distance: 136 - 141: 26.139 distance: 138 - 139: 30.625 distance: 138 - 140: 32.035