Starting phenix.real_space_refine on Wed Nov 19 22:27:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.map" model { file = "/net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cs2_7582/11_2025/6cs2_7582.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 148 5.16 5 C 17677 2.51 5 N 4480 2.21 5 O 5553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27858 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 6914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6914 Classifications: {'peptide': 891} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 848} Chain breaks: 5 Chain: "B" Number of atoms: 8405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8405 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1020} Chain breaks: 6 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 6927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6927 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 850} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4431 Classifications: {'peptide': 544} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 520} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.91, per 1000 atoms: 0.25 Number of scatterers: 27858 At special positions: 0 Unit cell: (189.52, 149.35, 231.75, 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 148 16.00 O 5553 8.00 N 4480 7.00 C 17677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 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 524 " - pdb=" SG CYS A 576 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.02 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.02 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 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=2.04 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=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 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 524 " - pdb=" SG CYS C 576 " distance=2.02 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1308 " - " ASN A 589 " " NAG B1310 " - " ASN B 589 " " NAG B1320 " - " ASN B1056 " " NAG C1309 " - " ASN C 589 " " NAG C1320 " - " ASN C1056 " " NAG E 1 " - " ASN A 269 " " NAG F 1 " - " ASN A 318 " " NAG G 1 " - " ASN A 691 " " NAG H 1 " - " ASN A 699 " " NAG I 1 " - " ASN A 783 " " NAG J 1 " - " ASN A1056 " " NAG K 1 " - " ASN A1080 " " NAG L 1 " - " ASN A1116 " " NAG M 1 " - " ASN A 602 " " NAG N 1 " - " ASN B 65 " " NAG O 1 " - " ASN B 269 " " NAG P 1 " - " ASN B 318 " " NAG Q 1 " - " ASN B 602 " " NAG R 1 " - " ASN B 691 " " NAG S 1 " - " ASN B 783 " " NAG T 1 " - " ASN B 699 " " NAG U 1 " - " ASN B1080 " " NAG V 1 " - " ASN B1116 " " NAG W 1 " - " ASN C 65 " " NAG X 1 " - " ASN C 269 " " NAG Y 1 " - " ASN C 318 " " NAG Z 1 " - " ASN C 691 " " NAG a 1 " - " ASN C 699 " " NAG b 1 " - " ASN C 783 " " NAG c 1 " - " ASN C1116 " " NAG d 1 " - " ASN C 602 " " NAG e 1 " - " ASN C1080 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6390 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 45 sheets defined 31.6% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.606A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 removed outlier: 3.639A pdb=" N TYR A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.627A pdb=" N ALA A 732 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.584A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 806 removed outlier: 4.117A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 864 removed outlier: 3.607A pdb=" N SER A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 864 " --> pdb=" O VAL A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.857A pdb=" N GLY A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 3.552A pdb=" N PHE A 888 " --> pdb=" O MET A 884 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN A 889 " --> pdb=" O ALA A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.167A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 923 removed outlier: 4.063A pdb=" N THR A 921 " --> pdb=" O GLN A 917 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 923 " --> pdb=" O SER A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.520A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) 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 962 through 966 removed outlier: 3.658A pdb=" N LEU A 966 " --> pdb=" O LEU A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1014 removed outlier: 3.855A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A1012 " --> pdb=" O ALA A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1129 removed outlier: 4.135A pdb=" N ASP A1128 " --> pdb=" O PRO A1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.513A pdb=" N LYS B 287 " --> pdb=" O LEU B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.612A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 removed outlier: 4.153A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 612 Processing helix chain 'B' and resid 720 through 725 Processing helix chain 'B' and resid 728 through 736 removed outlier: 3.612A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) 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 764 removed outlier: 4.183A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 749 " --> pdb=" O LEU B 745 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 761 " --> pdb=" O ASP B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.886A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 864 Processing helix chain 'B' and resid 867 through 872 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.623A pdb=" N ARG B 887 " --> pdb=" O GLN B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 900 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.626A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.743A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 939 " --> pdb=" O ASN B 935 " (cutoff:3.500A) 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 965 removed outlier: 3.735A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 1014 removed outlier: 4.281A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1123 through 1127 removed outlier: 3.730A pdb=" N GLU B1126 " --> pdb=" O LEU B1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 604 through 613 Processing helix chain 'C' and resid 729 through 735 Processing helix chain 'C' and resid 736 through 739 removed outlier: 4.301A pdb=" N GLY C 739 " --> pdb=" O LEU C 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 736 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.508A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 removed outlier: 3.769A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 removed outlier: 3.744A pdb=" N ALA C 864 " --> pdb=" O VAL C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 873 Processing helix chain 'C' and resid 879 through 892 removed outlier: 3.827A pdb=" N ARG C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE C 888 " --> pdb=" O MET C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.339A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 920 removed outlier: 3.511A pdb=" N ALA C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 950 removed outlier: 3.620A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER C 949 " --> pdb=" O VAL C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1016 removed outlier: 3.691A pdb=" N ALA C 971 " --> pdb=" O ASP C 967 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 975 " --> pdb=" O ALA C 971 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 976 " --> pdb=" O GLU C 972 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C1002 " --> pdb=" O ALA C 998 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS C1014 " --> pdb=" O LYS C1010 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1127 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.640A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 3.635A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.609A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.721A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.536A pdb=" N SER D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.503A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 3.771A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.644A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.577A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 298 removed outlier: 3.770A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.627A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.516A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 406 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 465 removed outlier: 3.683A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.590A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN D 508 " --> pdb=" O PHE D 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 503 through 508' Processing helix chain 'D' and resid 513 through 534 removed outlier: 3.787A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 557 removed outlier: 3.625A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 33 removed outlier: 4.049A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.035A pdb=" N PHE A 47 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.437A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 151 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 139 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 141 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A 147 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.873A pdb=" N PHE A 231 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 12.467A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 12.963A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.990A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 239 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL A 140 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN A 129 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N CYS A 159 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU A 131 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N PHE A 157 " --> pdb=" O GLU A 131 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N CYS A 133 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 9.841A pdb=" N ASN A 155 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ASN A 135 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 153 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A 151 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 139 " --> pdb=" O HIS A 149 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER A 141 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLN A 147 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 615 through 616 removed outlier: 4.138A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 524 through 525 removed outlier: 3.881A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA9, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.295A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 693 through 695 Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 704 removed outlier: 5.886A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'A' and resid 821 through 823 Processing sheet with id=AB6, first strand: chain 'A' and resid 1062 through 1064 Processing sheet with id=AB7, first strand: chain 'A' and resid 1068 through 1072 removed outlier: 4.262A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 34 removed outlier: 7.805A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.991A 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: 6.591A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 137 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 149 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 139 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN B 147 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.960A pdb=" N PHE B 231 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 12.841A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 13.034A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 10.034A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 123 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TYR B 163 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 125 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 161 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA B 127 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 159 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 155 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N CYS B 133 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE B 153 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASN B 135 " --> pdb=" O MET B 151 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N MET B 151 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N PHE B 137 " --> pdb=" O HIS B 149 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N HIS B 149 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA B 139 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN B 147 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.657A pdb=" N THR B 616 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 581 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY B 579 " --> pdb=" O PHE B 305 " (cutoff:3.500A) removed outlier: 3.960A 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: 6.461A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 574 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 343 through 345 removed outlier: 3.583A pdb=" N TRP B 423 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC7, first strand: chain 'B' and resid 640 through 646 removed outlier: 6.024A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.629A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.629A pdb=" N GLN B1053 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N PHE B 700 " --> pdb=" O PRO B1051 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE B 702 " --> pdb=" O TYR B1049 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B1049 " --> pdb=" O ILE B 702 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE B 704 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL B1047 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 706 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B1045 " --> pdb=" O THR B 706 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 708 " --> pdb=" O VAL B1043 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B1043 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLY B1041 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD2, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD3, first strand: chain 'B' and resid 821 through 822 removed outlier: 3.510A pdb=" N ALA B 834 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 4.914A pdb=" N VAL B1104 " --> pdb=" O PHE B1071 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE B1071 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLY B1106 " --> pdb=" O ALA B1069 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS B1065 " --> pdb=" O LYS B1068 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR B1070 " --> pdb=" O ILE B1063 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.086A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.842A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.018A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 12.654A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N SER C 239 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL C 140 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.500A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 615 through 616 removed outlier: 4.261A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 640 through 646 removed outlier: 5.894A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 693 through 695 removed outlier: 4.638A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 699 through 710 removed outlier: 7.341A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AE5, first strand: chain 'C' and resid 821 through 822 Processing sheet with id=AE6, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.598A pdb=" N TYR C1070 " --> pdb=" O ILE C1063 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AE8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.457A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.741A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3057 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: 6.46 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8730 1.34 - 1.46: 7226 1.46 - 1.59: 12312 1.59 - 1.71: 3 1.71 - 1.83: 214 Bond restraints: 28485 Sorted by residual: bond pdb=" C GLN B1124 " pdb=" N PRO B1125 " ideal model delta sigma weight residual 1.337 1.390 -0.053 9.80e-03 1.04e+04 2.93e+01 bond pdb=" N PRO B 493 " pdb=" CD PRO B 493 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" C5 MAN I 4 " pdb=" O5 MAN I 4 " ideal model delta sigma weight residual 1.418 1.483 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 MAN U 4 " pdb=" C2 MAN U 4 " ideal model delta sigma weight residual 1.526 1.588 -0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" C5 MAN e 4 " pdb=" O5 MAN e 4 " ideal model delta sigma weight residual 1.418 1.473 -0.055 2.00e-02 2.50e+03 7.55e+00 ... (remaining 28480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 37343 2.29 - 4.59: 1160 4.59 - 6.88: 196 6.88 - 9.18: 30 9.18 - 11.47: 6 Bond angle restraints: 38735 Sorted by residual: angle pdb=" N SER D 502 " pdb=" CA SER D 502 " pdb=" C SER D 502 " ideal model delta sigma weight residual 111.82 100.82 11.00 1.16e+00 7.43e-01 8.99e+01 angle pdb=" N PHE D 504 " pdb=" CA PHE D 504 " pdb=" C PHE D 504 " ideal model delta sigma weight residual 112.38 119.63 -7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" C VAL B1022 " pdb=" N ASP B1023 " pdb=" CA ASP B1023 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C SER B 346 " pdb=" N ASN B 347 " pdb=" CA ASN B 347 " ideal model delta sigma weight residual 121.54 130.80 -9.26 1.91e+00 2.74e-01 2.35e+01 angle pdb=" N PRO A 968 " pdb=" CA PRO A 968 " pdb=" C PRO A 968 " ideal model delta sigma weight residual 110.70 116.49 -5.79 1.22e+00 6.72e-01 2.26e+01 ... (remaining 38730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.77: 17429 22.77 - 45.55: 417 45.55 - 68.32: 74 68.32 - 91.09: 120 91.09 - 113.87: 80 Dihedral angle restraints: 18120 sinusoidal: 8205 harmonic: 9915 Sorted by residual: dihedral pdb=" CA PHE C 83 " pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta harmonic sigma weight residual -180.00 -134.02 -45.98 0 5.00e+00 4.00e-02 8.45e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -167.64 81.64 1 1.00e+01 1.00e-02 8.20e+01 dihedral pdb=" CB CYS C1014 " pdb=" SG CYS C1014 " pdb=" SG CYS C1025 " pdb=" CB CYS C1025 " ideal model delta sinusoidal sigma weight residual 93.00 167.37 -74.37 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 18117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3811 0.073 - 0.146: 716 0.146 - 0.219: 63 0.219 - 0.293: 21 0.293 - 0.366: 13 Chirality restraints: 4624 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 691 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CB ILE C 955 " pdb=" CA ILE C 955 " pdb=" CG1 ILE C 955 " pdb=" CG2 ILE C 955 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4621 not shown) Planarity restraints: 4914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C PHE C 83 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.027 2.00e-02 2.50e+03 pdb=" N LYS C 84 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 83 " 0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C PHE A 83 " -0.069 2.00e-02 2.50e+03 pdb=" O PHE A 83 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS A 84 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 83 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.38e+00 pdb=" C PHE B 83 " -0.050 2.00e-02 2.50e+03 pdb=" O PHE B 83 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS B 84 " 0.017 2.00e-02 2.50e+03 ... (remaining 4911 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 264 2.56 - 3.14: 21901 3.14 - 3.73: 42955 3.73 - 4.31: 59734 4.31 - 4.90: 95606 Nonbonded interactions: 220460 Sorted by model distance: nonbonded pdb=" OG1 THR B 425 " pdb=" O PRO B 493 " model vdw 1.972 3.040 nonbonded pdb=" O LEU A 966 " pdb=" OD1 ASP A 967 " model vdw 2.018 3.040 nonbonded pdb=" O ASP C 727 " pdb=" OD1 ASP C 727 " model vdw 2.033 3.040 nonbonded pdb=" O ASP D 499 " pdb=" OG SER D 502 " model vdw 2.084 3.040 nonbonded pdb=" O VAL B 354 " pdb=" OG SER B 358 " model vdw 2.237 3.040 ... (remaining 220455 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 18 through 318 or (resid 515 and (name N or name CA or nam \ e C or name O or name CB )) or resid 516 through 1308)) selection = (chain 'C' and (resid 18 through 663 or resid 672 through 808 or resid 818 throu \ gh 1320)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'Y' selection = chain 'Z' selection = chain 'c' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' } 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: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.310 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.007 0.065 28616 Z= 0.320 Angle : 1.006 11.474 39088 Z= 0.508 Chirality : 0.059 0.366 4624 Planarity : 0.006 0.060 4881 Dihedral : 15.289 113.866 11610 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.02 % Favored : 92.93 % Rotamer: Outliers : 0.24 % Allowed : 1.69 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 3364 helix: -3.00 (0.11), residues: 953 sheet: -1.76 (0.19), residues: 659 loop : -2.81 (0.12), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 996 TYR 0.030 0.003 TYR B 481 PHE 0.025 0.003 PHE A 805 TRP 0.029 0.003 TRP D 163 HIS 0.016 0.002 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00664 (28485) covalent geometry : angle 0.97141 (38735) SS BOND : bond 0.00484 ( 40) SS BOND : angle 1.75544 ( 80) hydrogen bonds : bond 0.28318 ( 1085) hydrogen bonds : angle 9.84598 ( 3057) link_ALPHA1-3 : bond 0.00377 ( 10) link_ALPHA1-3 : angle 2.13722 ( 30) link_ALPHA1-6 : bond 0.00564 ( 1) link_ALPHA1-6 : angle 1.77166 ( 3) link_BETA1-4 : bond 0.00888 ( 47) link_BETA1-4 : angle 2.90255 ( 141) link_NAG-ASN : bond 0.00889 ( 33) link_NAG-ASN : angle 3.76470 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 230 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8650 (mp0) REVERT: A 263 MET cc_start: 0.8672 (ttp) cc_final: 0.8280 (tmm) REVERT: A 264 LEU cc_start: 0.9564 (mt) cc_final: 0.9286 (mt) REVERT: A 312 ASP cc_start: 0.8584 (t0) cc_final: 0.8293 (m-30) REVERT: A 884 MET cc_start: 0.9627 (mmm) cc_final: 0.9392 (mmm) REVERT: A 1011 MET cc_start: 0.8849 (ptm) cc_final: 0.8591 (ppp) REVERT: A 1032 MET cc_start: 0.8402 (ttm) cc_final: 0.8169 (ttm) REVERT: B 37 MET cc_start: 0.9319 (mtp) cc_final: 0.9004 (mpp) REVERT: B 263 MET cc_start: 0.8391 (ttp) cc_final: 0.7921 (tpp) REVERT: B 615 LEU cc_start: 0.9354 (tp) cc_final: 0.9154 (tt) REVERT: B 709 MET cc_start: 0.9093 (mtp) cc_final: 0.8819 (mtp) REVERT: B 927 LEU cc_start: 0.9496 (mp) cc_final: 0.9182 (tt) REVERT: B 930 LEU cc_start: 0.9737 (mt) cc_final: 0.9434 (mp) REVERT: C 194 LEU cc_start: 0.9424 (tp) cc_final: 0.9139 (mm) REVERT: C 263 MET cc_start: 0.8527 (ttp) cc_final: 0.8305 (tpp) REVERT: C 932 ASP cc_start: 0.9167 (t0) cc_final: 0.8825 (t0) REVERT: D 455 MET cc_start: 0.6177 (tmm) cc_final: 0.5738 (tmm) outliers start: 7 outliers final: 1 residues processed: 237 average time/residue: 0.2179 time to fit residues: 77.9015 Evaluate side-chains 128 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 30.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 756 GLN A 974 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 122 ASN B 135 ASN B 201 GLN B 330 ASN B 445 HIS B 473 ASN B 549 GLN B 733 ASN B 835 GLN B 951 ASN B 987 GLN B1088 GLN C 70 HIS C 135 ASN C 201 GLN C 630 GLN C 877 GLN C 917 GLN C 931 GLN C 939 GLN C1088 GLN D 33 ASN D 239 HIS D 345 HIS D 526 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.052825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.035977 restraints weight = 271242.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.037015 restraints weight = 167569.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.037688 restraints weight = 120758.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.038116 restraints weight = 97038.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.038401 restraints weight = 84368.370| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 28616 Z= 0.141 Angle : 0.696 9.302 39088 Z= 0.348 Chirality : 0.046 0.271 4624 Planarity : 0.005 0.076 4881 Dihedral : 13.373 87.244 5483 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.13), residues: 3364 helix: -1.16 (0.15), residues: 974 sheet: -1.32 (0.19), residues: 623 loop : -2.42 (0.13), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 965 TYR 0.022 0.002 TYR D 385 PHE 0.018 0.001 PHE A 805 TRP 0.017 0.001 TRP D 163 HIS 0.006 0.001 HIS D 239 Details of bonding type rmsd covalent geometry : bond 0.00289 (28485) covalent geometry : angle 0.66839 (38735) SS BOND : bond 0.00272 ( 40) SS BOND : angle 1.23228 ( 80) hydrogen bonds : bond 0.05581 ( 1085) hydrogen bonds : angle 6.40107 ( 3057) link_ALPHA1-3 : bond 0.00845 ( 10) link_ALPHA1-3 : angle 2.26130 ( 30) link_ALPHA1-6 : bond 0.01326 ( 1) link_ALPHA1-6 : angle 2.63684 ( 3) link_BETA1-4 : bond 0.00507 ( 47) link_BETA1-4 : angle 2.44826 ( 141) link_NAG-ASN : bond 0.00402 ( 33) link_NAG-ASN : angle 2.27298 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8662 (mm-30) REVERT: A 263 MET cc_start: 0.8967 (ttp) cc_final: 0.8542 (tmm) REVERT: A 264 LEU cc_start: 0.9592 (mt) cc_final: 0.8979 (mt) REVERT: A 312 ASP cc_start: 0.8639 (t0) cc_final: 0.8282 (m-30) REVERT: A 966 LEU cc_start: 0.9413 (tt) cc_final: 0.9096 (mt) REVERT: B 37 MET cc_start: 0.9230 (mtp) cc_final: 0.8882 (mpp) REVERT: B 263 MET cc_start: 0.7982 (ttp) cc_final: 0.7512 (tpp) REVERT: B 709 MET cc_start: 0.9084 (mtp) cc_final: 0.8823 (mtp) REVERT: B 762 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8344 (mt-10) REVERT: B 930 LEU cc_start: 0.9685 (mt) cc_final: 0.9444 (mp) REVERT: C 194 LEU cc_start: 0.9407 (tp) cc_final: 0.9147 (mm) REVERT: C 888 PHE cc_start: 0.9419 (m-80) cc_final: 0.9211 (m-80) REVERT: C 932 ASP cc_start: 0.9075 (t0) cc_final: 0.8680 (t0) REVERT: D 462 MET cc_start: 0.4591 (ptp) cc_final: 0.4272 (ptt) REVERT: D 557 MET cc_start: 0.7816 (ppp) cc_final: 0.7510 (ppp) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.1972 time to fit residues: 54.7563 Evaluate side-chains 129 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 136 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 304 optimal weight: 50.0000 chunk 242 optimal weight: 20.0000 chunk 210 optimal weight: 2.9990 chunk 162 optimal weight: 0.0070 chunk 12 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 135 ASN A 201 GLN A 733 ASN A 984 GLN A 987 GLN A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 835 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 ASN B 984 GLN B 992 GLN B1005 ASN B1030 HIS B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS C 135 ASN C 630 GLN C 917 GLN C1088 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.051025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.034098 restraints weight = 288692.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.035113 restraints weight = 178681.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.035753 restraints weight = 129388.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.036080 restraints weight = 105067.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.036391 restraints weight = 92304.069| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28616 Z= 0.232 Angle : 0.736 8.545 39088 Z= 0.366 Chirality : 0.046 0.216 4624 Planarity : 0.005 0.077 4881 Dihedral : 9.843 71.921 5483 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.03 % Allowed : 2.44 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.13), residues: 3364 helix: -0.41 (0.15), residues: 984 sheet: -1.38 (0.19), residues: 641 loop : -2.34 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 965 TYR 0.018 0.002 TYR A 886 PHE 0.023 0.002 PHE B 741 TRP 0.020 0.002 TRP D 478 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00475 (28485) covalent geometry : angle 0.71189 (38735) SS BOND : bond 0.00666 ( 40) SS BOND : angle 1.30581 ( 80) hydrogen bonds : bond 0.04967 ( 1085) hydrogen bonds : angle 6.19245 ( 3057) link_ALPHA1-3 : bond 0.00799 ( 10) link_ALPHA1-3 : angle 1.96205 ( 30) link_ALPHA1-6 : bond 0.01331 ( 1) link_ALPHA1-6 : angle 2.63400 ( 3) link_BETA1-4 : bond 0.00556 ( 47) link_BETA1-4 : angle 2.30732 ( 141) link_NAG-ASN : bond 0.00574 ( 33) link_NAG-ASN : angle 2.32768 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6877 (mmp) cc_final: 0.6322 (tpp) REVERT: A 184 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8308 (mp0) REVERT: A 263 MET cc_start: 0.9174 (ttp) cc_final: 0.8726 (tmm) REVERT: A 264 LEU cc_start: 0.9651 (mt) cc_final: 0.9048 (mt) REVERT: A 884 MET cc_start: 0.9500 (mmp) cc_final: 0.9193 (mmp) REVERT: A 966 LEU cc_start: 0.9420 (tt) cc_final: 0.9082 (mt) REVERT: B 37 MET cc_start: 0.9314 (mtp) cc_final: 0.8868 (mpp) REVERT: B 188 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8933 (ttmt) REVERT: B 263 MET cc_start: 0.8231 (ttp) cc_final: 0.7733 (tpp) REVERT: B 709 MET cc_start: 0.9145 (mtp) cc_final: 0.8908 (mtp) REVERT: C 107 MET cc_start: 0.5207 (mmt) cc_final: 0.4916 (mmt) REVERT: C 151 MET cc_start: 0.6467 (mtp) cc_final: 0.6258 (mtp) REVERT: C 194 LEU cc_start: 0.9556 (tp) cc_final: 0.9196 (mm) REVERT: C 932 ASP cc_start: 0.9355 (t0) cc_final: 0.9005 (t0) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1946 time to fit residues: 42.4184 Evaluate side-chains 109 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 256 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 276 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A1088 GLN B 135 ASN B 201 GLN B 381 ASN B 835 GLN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 ASN C 917 GLN C1088 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.034150 restraints weight = 267617.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.035179 restraints weight = 165458.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.035808 restraints weight = 119743.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036144 restraints weight = 96846.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036461 restraints weight = 84916.408| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28616 Z= 0.160 Angle : 0.649 9.019 39088 Z= 0.323 Chirality : 0.045 0.203 4624 Planarity : 0.004 0.049 4881 Dihedral : 8.033 62.167 5483 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.14), residues: 3364 helix: 0.01 (0.16), residues: 985 sheet: -1.29 (0.19), residues: 642 loop : -2.19 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 306 TYR 0.016 0.001 TYR A 886 PHE 0.018 0.001 PHE A 805 TRP 0.014 0.001 TRP B 868 HIS 0.005 0.001 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00334 (28485) covalent geometry : angle 0.62672 (38735) SS BOND : bond 0.00403 ( 40) SS BOND : angle 1.20301 ( 80) hydrogen bonds : bond 0.04400 ( 1085) hydrogen bonds : angle 5.90982 ( 3057) link_ALPHA1-3 : bond 0.00861 ( 10) link_ALPHA1-3 : angle 1.86500 ( 30) link_ALPHA1-6 : bond 0.01223 ( 1) link_ALPHA1-6 : angle 2.45595 ( 3) link_BETA1-4 : bond 0.00559 ( 47) link_BETA1-4 : angle 2.10346 ( 141) link_NAG-ASN : bond 0.00289 ( 33) link_NAG-ASN : angle 1.96852 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7085 (mmp) cc_final: 0.6669 (tpp) REVERT: A 184 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8239 (mp0) REVERT: A 263 MET cc_start: 0.9211 (ttp) cc_final: 0.8763 (tmm) REVERT: A 264 LEU cc_start: 0.9648 (mt) cc_final: 0.9037 (mt) REVERT: A 966 LEU cc_start: 0.9431 (tt) cc_final: 0.9108 (mt) REVERT: A 984 GLN cc_start: 0.9182 (mm110) cc_final: 0.8890 (mm-40) REVERT: B 37 MET cc_start: 0.9214 (mtp) cc_final: 0.8800 (mpp) REVERT: B 188 LYS cc_start: 0.9158 (mtmt) cc_final: 0.8891 (ttmt) REVERT: B 263 MET cc_start: 0.8182 (ttp) cc_final: 0.7701 (tpp) REVERT: B 709 MET cc_start: 0.9131 (mtp) cc_final: 0.8928 (mtp) REVERT: C 107 MET cc_start: 0.5408 (mmt) cc_final: 0.5080 (mmt) REVERT: C 194 LEU cc_start: 0.9514 (tp) cc_final: 0.9174 (mm) REVERT: C 888 PHE cc_start: 0.9547 (m-80) cc_final: 0.9333 (m-80) REVERT: C 932 ASP cc_start: 0.9354 (t0) cc_final: 0.8990 (t0) REVERT: D 462 MET cc_start: 0.4802 (ptt) cc_final: 0.4445 (ptt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1880 time to fit residues: 41.9274 Evaluate side-chains 110 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 145 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 257 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 331 optimal weight: 30.0000 chunk 317 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 290 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 282 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 149 HIS A 201 GLN ** A1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 381 ASN B 759 ASN B 835 GLN B 877 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 992 GLN B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.050156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.033232 restraints weight = 289558.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.034240 restraints weight = 179895.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.034857 restraints weight = 131171.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.035178 restraints weight = 106381.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035484 restraints weight = 93413.951| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28616 Z= 0.263 Angle : 0.749 9.690 39088 Z= 0.374 Chirality : 0.045 0.217 4624 Planarity : 0.004 0.056 4881 Dihedral : 7.357 55.944 5483 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.14), residues: 3364 helix: -0.09 (0.16), residues: 985 sheet: -1.19 (0.20), residues: 616 loop : -2.28 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 99 TYR 0.027 0.002 TYR D 217 PHE 0.020 0.002 PHE A 782 TRP 0.019 0.002 TRP D 477 HIS 0.010 0.002 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00544 (28485) covalent geometry : angle 0.72647 (38735) SS BOND : bond 0.00402 ( 40) SS BOND : angle 1.43597 ( 80) hydrogen bonds : bond 0.04540 ( 1085) hydrogen bonds : angle 6.10573 ( 3057) link_ALPHA1-3 : bond 0.00743 ( 10) link_ALPHA1-3 : angle 2.09463 ( 30) link_ALPHA1-6 : bond 0.01228 ( 1) link_ALPHA1-6 : angle 2.59365 ( 3) link_BETA1-4 : bond 0.00533 ( 47) link_BETA1-4 : angle 2.05987 ( 141) link_NAG-ASN : bond 0.00679 ( 33) link_NAG-ASN : angle 2.38842 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8138 (mp0) REVERT: A 263 MET cc_start: 0.9140 (ttp) cc_final: 0.8654 (tmm) REVERT: A 264 LEU cc_start: 0.9594 (mt) cc_final: 0.9007 (mt) REVERT: B 37 MET cc_start: 0.9114 (mtp) cc_final: 0.8732 (mpp) REVERT: B 107 MET cc_start: 0.6985 (mmt) cc_final: 0.6676 (mmt) REVERT: B 188 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8574 (tttt) REVERT: B 263 MET cc_start: 0.8068 (ttp) cc_final: 0.7522 (tpp) REVERT: B 886 TYR cc_start: 0.9212 (t80) cc_final: 0.8741 (t80) REVERT: C 107 MET cc_start: 0.5550 (mmt) cc_final: 0.5248 (mmt) REVERT: C 151 MET cc_start: 0.6981 (mtp) cc_final: 0.6738 (mtp) REVERT: C 194 LEU cc_start: 0.9472 (tp) cc_final: 0.9101 (mm) REVERT: C 758 ARG cc_start: 0.8613 (mmp80) cc_final: 0.8010 (mmp80) REVERT: C 932 ASP cc_start: 0.9343 (t0) cc_final: 0.9005 (t0) REVERT: D 190 MET cc_start: 0.7247 (mmt) cc_final: 0.7021 (tpp) REVERT: D 455 MET cc_start: 0.6127 (tmm) cc_final: 0.4796 (tmm) REVERT: D 462 MET cc_start: 0.5031 (ptt) cc_final: 0.4659 (ptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2027 time to fit residues: 40.9240 Evaluate side-chains 105 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 172 optimal weight: 8.9990 chunk 153 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 247 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 chunk 132 optimal weight: 40.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN A 756 GLN A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 835 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 974 GLN C1046 HIS C1088 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.050306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.033398 restraints weight = 274837.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034370 restraints weight = 172203.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.034967 restraints weight = 125612.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035335 restraints weight = 102024.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035544 restraints weight = 89094.811| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28616 Z= 0.202 Angle : 0.679 8.153 39088 Z= 0.339 Chirality : 0.044 0.218 4624 Planarity : 0.004 0.050 4881 Dihedral : 7.024 54.305 5483 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.14), residues: 3364 helix: 0.08 (0.16), residues: 980 sheet: -1.22 (0.20), residues: 611 loop : -2.21 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 761 TYR 0.019 0.002 TYR D 385 PHE 0.016 0.002 PHE A 782 TRP 0.014 0.002 TRP C 868 HIS 0.007 0.001 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00421 (28485) covalent geometry : angle 0.65919 (38735) SS BOND : bond 0.00539 ( 40) SS BOND : angle 1.43188 ( 80) hydrogen bonds : bond 0.04296 ( 1085) hydrogen bonds : angle 5.92989 ( 3057) link_ALPHA1-3 : bond 0.00819 ( 10) link_ALPHA1-3 : angle 1.78629 ( 30) link_ALPHA1-6 : bond 0.01127 ( 1) link_ALPHA1-6 : angle 2.19275 ( 3) link_BETA1-4 : bond 0.00501 ( 47) link_BETA1-4 : angle 1.87886 ( 141) link_NAG-ASN : bond 0.00445 ( 33) link_NAG-ASN : angle 2.02964 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9153 (ttp) cc_final: 0.8751 (tmm) REVERT: A 264 LEU cc_start: 0.9598 (mt) cc_final: 0.8988 (mt) REVERT: A 886 TYR cc_start: 0.8887 (t80) cc_final: 0.8577 (t80) REVERT: A 966 LEU cc_start: 0.9366 (tt) cc_final: 0.9111 (mt) REVERT: B 37 MET cc_start: 0.9042 (mtp) cc_final: 0.8659 (mpp) REVERT: B 188 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8484 (tttt) REVERT: B 263 MET cc_start: 0.8051 (ttp) cc_final: 0.7551 (tpp) REVERT: B 886 TYR cc_start: 0.9249 (t80) cc_final: 0.8730 (t80) REVERT: C 107 MET cc_start: 0.5496 (mmt) cc_final: 0.5105 (mmt) REVERT: C 194 LEU cc_start: 0.9444 (tp) cc_final: 0.9081 (mm) REVERT: C 679 MET cc_start: 0.8831 (tpp) cc_final: 0.8627 (tpp) REVERT: C 932 ASP cc_start: 0.9349 (t0) cc_final: 0.8999 (t0) REVERT: D 190 MET cc_start: 0.7267 (mmt) cc_final: 0.7061 (tpp) REVERT: D 408 MET cc_start: 0.5428 (mpp) cc_final: 0.5094 (mmt) REVERT: D 462 MET cc_start: 0.4948 (ptt) cc_final: 0.4724 (ptt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1949 time to fit residues: 38.8208 Evaluate side-chains 104 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 233 optimal weight: 5.9990 chunk 327 optimal weight: 30.0000 chunk 336 optimal weight: 8.9990 chunk 278 optimal weight: 10.0000 chunk 75 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 225 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 993 GLN A1088 GLN B 201 GLN B 835 GLN B 984 GLN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1088 GLN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034232 restraints weight = 266578.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.035252 restraints weight = 163931.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.035885 restraints weight = 117007.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036229 restraints weight = 94085.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036540 restraints weight = 81844.976| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28616 Z= 0.120 Angle : 0.605 8.976 39088 Z= 0.300 Chirality : 0.043 0.194 4624 Planarity : 0.004 0.045 4881 Dihedral : 6.342 49.236 5483 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3364 helix: 0.47 (0.17), residues: 976 sheet: -1.13 (0.20), residues: 610 loop : -2.08 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.013 0.001 TYR B 491 PHE 0.016 0.001 PHE C 909 TRP 0.030 0.001 TRP B 868 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00257 (28485) covalent geometry : angle 0.58720 (38735) SS BOND : bond 0.00341 ( 40) SS BOND : angle 1.16440 ( 80) hydrogen bonds : bond 0.03969 ( 1085) hydrogen bonds : angle 5.56849 ( 3057) link_ALPHA1-3 : bond 0.00865 ( 10) link_ALPHA1-3 : angle 1.53561 ( 30) link_ALPHA1-6 : bond 0.01490 ( 1) link_ALPHA1-6 : angle 2.30328 ( 3) link_BETA1-4 : bond 0.00448 ( 47) link_BETA1-4 : angle 1.76197 ( 141) link_NAG-ASN : bond 0.00266 ( 33) link_NAG-ASN : angle 1.78007 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6930 (tpt) cc_final: 0.6513 (tpt) REVERT: A 263 MET cc_start: 0.9263 (ttp) cc_final: 0.8778 (tmm) REVERT: A 264 LEU cc_start: 0.9643 (mt) cc_final: 0.9028 (mt) REVERT: A 722 MET cc_start: 0.8429 (mmm) cc_final: 0.8100 (tmm) REVERT: A 886 TYR cc_start: 0.8967 (t80) cc_final: 0.8735 (t80) REVERT: A 966 LEU cc_start: 0.9405 (tt) cc_final: 0.9188 (mt) REVERT: A 984 GLN cc_start: 0.9210 (mm110) cc_final: 0.9001 (tp40) REVERT: A 1011 MET cc_start: 0.9134 (tmm) cc_final: 0.8902 (tmm) REVERT: B 37 MET cc_start: 0.9181 (mtp) cc_final: 0.8802 (mpp) REVERT: B 107 MET cc_start: 0.7168 (mmt) cc_final: 0.6875 (mmt) REVERT: B 151 MET cc_start: 0.5830 (mtt) cc_final: 0.5497 (mtt) REVERT: B 188 LYS cc_start: 0.8995 (mtmt) cc_final: 0.8542 (tttt) REVERT: B 263 MET cc_start: 0.8083 (ttp) cc_final: 0.7558 (tpp) REVERT: B 851 MET cc_start: 0.9340 (mtm) cc_final: 0.9127 (mtt) REVERT: C 107 MET cc_start: 0.5515 (mmt) cc_final: 0.5137 (mmt) REVERT: C 151 MET cc_start: 0.6522 (mtp) cc_final: 0.6319 (mtp) REVERT: C 194 LEU cc_start: 0.9467 (tp) cc_final: 0.9143 (mm) REVERT: C 679 MET cc_start: 0.8933 (tpp) cc_final: 0.8657 (tpp) REVERT: C 932 ASP cc_start: 0.9354 (t0) cc_final: 0.8980 (t0) REVERT: C 1011 MET cc_start: 0.9460 (tpp) cc_final: 0.9011 (tpp) REVERT: D 190 MET cc_start: 0.7253 (mmt) cc_final: 0.7039 (tpp) REVERT: D 408 MET cc_start: 0.5578 (mpp) cc_final: 0.5365 (mmm) REVERT: D 455 MET cc_start: 0.5984 (tmm) cc_final: 0.4511 (tmm) REVERT: D 462 MET cc_start: 0.5012 (ptt) cc_final: 0.4547 (ptt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1963 time to fit residues: 42.6406 Evaluate side-chains 104 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 284 optimal weight: 30.0000 chunk 128 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 318 optimal weight: 5.9990 chunk 268 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 201 GLN B 835 GLN B 992 GLN B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.051360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.034196 restraints weight = 268805.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.035213 restraints weight = 165558.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035863 restraints weight = 119355.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.036275 restraints weight = 95597.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.036490 restraints weight = 82755.005| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28616 Z= 0.117 Angle : 0.605 9.312 39088 Z= 0.299 Chirality : 0.043 0.196 4624 Planarity : 0.004 0.045 4881 Dihedral : 5.918 44.752 5483 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3364 helix: 0.61 (0.17), residues: 978 sheet: -1.03 (0.20), residues: 618 loop : -1.99 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 342 TYR 0.012 0.001 TYR C 886 PHE 0.015 0.001 PHE C 909 TRP 0.021 0.001 TRP B 868 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00254 (28485) covalent geometry : angle 0.58613 (38735) SS BOND : bond 0.00310 ( 40) SS BOND : angle 1.04355 ( 80) hydrogen bonds : bond 0.03803 ( 1085) hydrogen bonds : angle 5.43764 ( 3057) link_ALPHA1-3 : bond 0.00825 ( 10) link_ALPHA1-3 : angle 1.51707 ( 30) link_ALPHA1-6 : bond 0.01765 ( 1) link_ALPHA1-6 : angle 2.33911 ( 3) link_BETA1-4 : bond 0.00466 ( 47) link_BETA1-4 : angle 1.76005 ( 141) link_NAG-ASN : bond 0.00250 ( 33) link_NAG-ASN : angle 2.02453 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.6911 (tpt) cc_final: 0.6516 (tpt) REVERT: A 263 MET cc_start: 0.9284 (ttp) cc_final: 0.8831 (tpp) REVERT: A 264 LEU cc_start: 0.9642 (mt) cc_final: 0.9270 (mt) REVERT: A 713 MET cc_start: 0.8854 (ttp) cc_final: 0.8553 (tmm) REVERT: A 722 MET cc_start: 0.8474 (mmm) cc_final: 0.8099 (tmm) REVERT: A 886 TYR cc_start: 0.9059 (t80) cc_final: 0.8736 (t80) REVERT: A 966 LEU cc_start: 0.9429 (tt) cc_final: 0.9217 (mt) REVERT: B 37 MET cc_start: 0.9171 (mtp) cc_final: 0.8800 (mpp) REVERT: B 107 MET cc_start: 0.7126 (mmt) cc_final: 0.6843 (mmt) REVERT: B 188 LYS cc_start: 0.8948 (mtmt) cc_final: 0.8475 (tttt) REVERT: B 263 MET cc_start: 0.8074 (ttp) cc_final: 0.7560 (tpp) REVERT: B 851 MET cc_start: 0.9391 (mtm) cc_final: 0.9186 (mtt) REVERT: C 107 MET cc_start: 0.5538 (mmt) cc_final: 0.5170 (mmt) REVERT: C 151 MET cc_start: 0.6486 (mtp) cc_final: 0.6058 (mtp) REVERT: C 194 LEU cc_start: 0.9439 (tp) cc_final: 0.9144 (mm) REVERT: C 679 MET cc_start: 0.8952 (tpp) cc_final: 0.8661 (tpp) REVERT: C 932 ASP cc_start: 0.9339 (t0) cc_final: 0.8983 (t0) REVERT: C 1011 MET cc_start: 0.9495 (tpp) cc_final: 0.9083 (tpp) REVERT: D 190 MET cc_start: 0.7190 (mmt) cc_final: 0.6982 (tpp) REVERT: D 455 MET cc_start: 0.6029 (tmm) cc_final: 0.4617 (tmm) REVERT: D 462 MET cc_start: 0.5115 (ptt) cc_final: 0.4612 (ptt) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.1905 time to fit residues: 40.5154 Evaluate side-chains 108 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 2 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 237 optimal weight: 0.0670 chunk 321 optimal weight: 7.9990 chunk 308 optimal weight: 40.0000 chunk 243 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 322 optimal weight: 9.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.050342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.033579 restraints weight = 277870.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.034550 restraints weight = 174754.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035166 restraints weight = 126695.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035469 restraints weight = 102221.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035775 restraints weight = 90010.190| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28616 Z= 0.204 Angle : 0.673 12.560 39088 Z= 0.334 Chirality : 0.043 0.195 4624 Planarity : 0.004 0.049 4881 Dihedral : 6.015 40.001 5483 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3364 helix: 0.52 (0.17), residues: 979 sheet: -1.06 (0.20), residues: 612 loop : -2.00 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 887 TYR 0.020 0.002 TYR D 50 PHE 0.019 0.002 PHE D 315 TRP 0.018 0.002 TRP B 340 HIS 0.010 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00429 (28485) covalent geometry : angle 0.65563 (38735) SS BOND : bond 0.00334 ( 40) SS BOND : angle 1.27281 ( 80) hydrogen bonds : bond 0.03934 ( 1085) hydrogen bonds : angle 5.64548 ( 3057) link_ALPHA1-3 : bond 0.00639 ( 10) link_ALPHA1-3 : angle 1.67497 ( 30) link_ALPHA1-6 : bond 0.01340 ( 1) link_ALPHA1-6 : angle 2.18710 ( 3) link_BETA1-4 : bond 0.00465 ( 47) link_BETA1-4 : angle 1.80114 ( 141) link_NAG-ASN : bond 0.00477 ( 33) link_NAG-ASN : angle 1.97858 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7164 (tpt) cc_final: 0.6664 (tpt) REVERT: A 263 MET cc_start: 0.9212 (ttp) cc_final: 0.8701 (tmm) REVERT: A 264 LEU cc_start: 0.9597 (mt) cc_final: 0.8986 (mt) REVERT: A 713 MET cc_start: 0.8908 (ttp) cc_final: 0.8507 (tmm) REVERT: A 722 MET cc_start: 0.8320 (mmm) cc_final: 0.7982 (tmm) REVERT: A 886 TYR cc_start: 0.8895 (t80) cc_final: 0.8614 (t80) REVERT: A 966 LEU cc_start: 0.9353 (tt) cc_final: 0.9114 (mt) REVERT: B 37 MET cc_start: 0.9029 (mtp) cc_final: 0.8735 (mpp) REVERT: B 107 MET cc_start: 0.7005 (mmt) cc_final: 0.6725 (mmt) REVERT: B 151 MET cc_start: 0.4351 (mtt) cc_final: 0.3336 (ppp) REVERT: B 188 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8335 (mtpt) REVERT: B 263 MET cc_start: 0.8073 (ttp) cc_final: 0.7593 (tpp) REVERT: C 107 MET cc_start: 0.5581 (mmt) cc_final: 0.5234 (mmt) REVERT: C 151 MET cc_start: 0.6642 (mtp) cc_final: 0.6357 (mtp) REVERT: C 194 LEU cc_start: 0.9385 (tp) cc_final: 0.9078 (mm) REVERT: C 679 MET cc_start: 0.8767 (tpp) cc_final: 0.8531 (tpp) REVERT: C 932 ASP cc_start: 0.9320 (t0) cc_final: 0.8956 (t0) REVERT: C 1011 MET cc_start: 0.9440 (tpp) cc_final: 0.8819 (tpp) REVERT: D 190 MET cc_start: 0.7167 (mmt) cc_final: 0.6966 (tpp) REVERT: D 455 MET cc_start: 0.6234 (tmm) cc_final: 0.4860 (tmm) REVERT: D 462 MET cc_start: 0.5163 (ptt) cc_final: 0.4694 (ptt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1904 time to fit residues: 38.3004 Evaluate side-chains 102 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 312 optimal weight: 4.9990 chunk 232 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 337 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 300 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 118 optimal weight: 20.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 201 GLN B 835 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C 993 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.050686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.033832 restraints weight = 274601.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034827 restraints weight = 171961.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.035377 restraints weight = 124310.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035807 restraints weight = 101079.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.036099 restraints weight = 87921.299| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28616 Z= 0.161 Angle : 0.649 11.099 39088 Z= 0.321 Chirality : 0.043 0.192 4624 Planarity : 0.004 0.051 4881 Dihedral : 5.918 40.818 5483 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3364 helix: 0.57 (0.17), residues: 972 sheet: -1.04 (0.20), residues: 612 loop : -1.96 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.028 0.001 TYR D 50 PHE 0.021 0.001 PHE D 315 TRP 0.018 0.002 TRP B 340 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00346 (28485) covalent geometry : angle 0.63076 (38735) SS BOND : bond 0.00357 ( 40) SS BOND : angle 1.52418 ( 80) hydrogen bonds : bond 0.03857 ( 1085) hydrogen bonds : angle 5.57465 ( 3057) link_ALPHA1-3 : bond 0.00672 ( 10) link_ALPHA1-3 : angle 1.59414 ( 30) link_ALPHA1-6 : bond 0.01533 ( 1) link_ALPHA1-6 : angle 2.17410 ( 3) link_BETA1-4 : bond 0.00460 ( 47) link_BETA1-4 : angle 1.72395 ( 141) link_NAG-ASN : bond 0.00336 ( 33) link_NAG-ASN : angle 1.87353 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6728 Ramachandran restraints generated. 3364 Oldfield, 0 Emsley, 3364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7113 (tpt) cc_final: 0.6870 (tpt) REVERT: A 263 MET cc_start: 0.9213 (ttp) cc_final: 0.8794 (tpp) REVERT: A 264 LEU cc_start: 0.9603 (mt) cc_final: 0.9230 (mt) REVERT: A 679 MET cc_start: 0.9009 (mmt) cc_final: 0.8770 (mmt) REVERT: A 713 MET cc_start: 0.8833 (ttp) cc_final: 0.8478 (tmm) REVERT: A 722 MET cc_start: 0.8184 (mmm) cc_final: 0.7874 (tmm) REVERT: A 770 MET cc_start: 0.8550 (mpp) cc_final: 0.7968 (mpp) REVERT: A 886 TYR cc_start: 0.8978 (t80) cc_final: 0.8576 (t80) REVERT: A 966 LEU cc_start: 0.9375 (tt) cc_final: 0.9152 (mt) REVERT: B 37 MET cc_start: 0.9010 (mtp) cc_final: 0.8725 (mpp) REVERT: B 107 MET cc_start: 0.6981 (mmt) cc_final: 0.6716 (mmt) REVERT: B 151 MET cc_start: 0.3995 (mtt) cc_final: 0.3181 (ppp) REVERT: B 188 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8421 (tttt) REVERT: B 263 MET cc_start: 0.8028 (ttp) cc_final: 0.7558 (tpp) REVERT: C 107 MET cc_start: 0.5640 (mmt) cc_final: 0.5327 (mmt) REVERT: C 151 MET cc_start: 0.6805 (mtp) cc_final: 0.6581 (mtp) REVERT: C 194 LEU cc_start: 0.9372 (tp) cc_final: 0.9098 (mm) REVERT: C 679 MET cc_start: 0.8795 (tpp) cc_final: 0.8569 (tpp) REVERT: C 932 ASP cc_start: 0.9298 (t0) cc_final: 0.8920 (t0) REVERT: C 1011 MET cc_start: 0.9389 (tpp) cc_final: 0.8736 (tpp) REVERT: D 190 MET cc_start: 0.7158 (mmt) cc_final: 0.6955 (tpp) REVERT: D 462 MET cc_start: 0.5134 (ptt) cc_final: 0.4592 (ptt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1878 time to fit residues: 36.9053 Evaluate side-chains 103 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 254 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 329 optimal weight: 30.0000 chunk 338 optimal weight: 20.0000 chunk 26 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 296 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 835 GLN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 917 GLN C1030 HIS ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.050625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.033823 restraints weight = 274583.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.034814 restraints weight = 171997.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.035380 restraints weight = 125110.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.035800 restraints weight = 101424.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.036020 restraints weight = 88430.497| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28616 Z= 0.157 Angle : 0.628 10.424 39088 Z= 0.312 Chirality : 0.043 0.190 4624 Planarity : 0.004 0.055 4881 Dihedral : 5.780 43.303 5483 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.14), residues: 3364 helix: 0.67 (0.17), residues: 971 sheet: -1.01 (0.21), residues: 612 loop : -1.95 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 887 TYR 0.016 0.001 TYR D 510 PHE 0.015 0.001 PHE C 909 TRP 0.017 0.002 TRP B 340 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00337 (28485) covalent geometry : angle 0.60999 (38735) SS BOND : bond 0.00329 ( 40) SS BOND : angle 1.41599 ( 80) hydrogen bonds : bond 0.03796 ( 1085) hydrogen bonds : angle 5.53169 ( 3057) link_ALPHA1-3 : bond 0.00615 ( 10) link_ALPHA1-3 : angle 1.60715 ( 30) link_ALPHA1-6 : bond 0.01208 ( 1) link_ALPHA1-6 : angle 1.86249 ( 3) link_BETA1-4 : bond 0.00455 ( 47) link_BETA1-4 : angle 1.72373 ( 141) link_NAG-ASN : bond 0.00355 ( 33) link_NAG-ASN : angle 1.82693 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.48 seconds wall clock time: 90 minutes 40.74 seconds (5440.74 seconds total)