Starting phenix.real_space_refine on Mon Sep 14 04:46:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_7582.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_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_7582/09_2026/6cs2_7582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_7582.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_7582.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_7582.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_7582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cs2_7582/09_2026/6cs2_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 6.27, per 1000 atoms: 0.23 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: 2.81 Conformation dependent library (CDL) restraints added in 1.3 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: 1.04 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: 7.94 Time building geometry restraints manager: 3.68 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 - 16.33: 15600 16.33 - 32.66: 516 32.66 - 48.99: 136 48.99 - 65.32: 9 65.32 - 81.64: 10 Dihedral angle restraints: 16271 sinusoidal: 6356 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 16268 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: 4.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 29.830 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 9.047 74.763 9761 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/Z covalent geometry : bond 0.00664 / 0.32 (28485) covalent geometry : angle 0.97141 / 0.50 (38735) SS BOND : bond 0.00484 / 0.30 ( 40) SS BOND : angle 1.75544 / 1.20 ( 80) hydrogen bonds : bond 0.28318 / 19.07 ( 1085) hydrogen bonds : angle 9.84598 / 6.74 ( 3057) link_ALPHA1-3 : bond 0.00377 / 0.21 ( 10) link_ALPHA1-3 : angle 2.13722 / 1.46 ( 30) link_ALPHA1-6 : bond 0.00564 / 0.30 ( 1) link_ALPHA1-6 : angle 1.77166 / 1.00 ( 3) link_BETA1-4 : bond 0.00888 / 0.54 ( 47) link_BETA1-4 : angle 2.90255 / 1.91 ( 141) link_NAG-ASN : bond 0.00889 / 0.64 ( 33) link_NAG-ASN : angle 3.76470 / 2.45 ( 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 : 0.989 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: 0.8850 (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 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: 0.2012 time to fit residues: 73.0664 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 : 0.971 ------------------------------------------------------------------------------- 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... A 201 GLN A 733 ASN 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.052788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035955 restraints weight = 270678.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.036970 restraints weight = 166306.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.037620 restraints weight = 120382.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.038077 restraints weight = 97359.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.038366 restraints weight = 84300.594| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 28616 Z= 0.140 Angle : 0.666 9.315 39088 Z= 0.342 Chirality : 0.044 0.242 4624 Planarity : 0.005 0.082 4881 Dihedral : 5.450 31.360 3634 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: -2.75 (0.13), residues: 3364 helix: -1.16 (0.15), residues: 975 sheet: -1.33 (0.20), residues: 613 loop : -2.44 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1001 TYR 0.022 0.001 TYR D 385 PHE 0.018 0.001 PHE A 805 TRP 0.016 0.001 TRP B 868 HIS 0.006 0.001 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (28485) covalent geometry : angle 0.64508 / 0.34 (38735) SS BOND : bond 0.00507 / 0.27 ( 40) SS BOND : angle 1.37081 / 0.91 ( 80) hydrogen bonds : bond 0.05675 / 3.83 ( 1085) hydrogen bonds : angle 6.39750 / 4.35 ( 3057) link_ALPHA1-3 : bond 0.00422 / 0.26 ( 10) link_ALPHA1-3 : angle 1.62993 / 1.12 ( 30) link_ALPHA1-6 : bond 0.01634 / 0.86 ( 1) link_ALPHA1-6 : angle 2.41943 / 1.35 ( 3) link_BETA1-4 : bond 0.00449 / 0.28 ( 47) link_BETA1-4 : angle 1.86177 / 1.22 ( 141) link_NAG-ASN : bond 0.00365 / 0.25 ( 33) link_NAG-ASN : angle 2.23934 / 1.53 ( 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 175 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 1.031 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: A 184 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8657 (mm-30) REVERT: A 263 MET cc_start: 0.8966 (ttp) cc_final: 0.8545 (tmm) REVERT: A 264 LEU cc_start: 0.9592 (mt) cc_final: 0.8978 (mt) REVERT: A 312 ASP cc_start: 0.8639 (t0) cc_final: 0.8282 (m-30) REVERT: A 966 LEU cc_start: 0.9411 (tt) cc_final: 0.9094 (mt) REVERT: B 37 MET cc_start: 0.9219 (mtp) cc_final: 0.8876 (mpp) REVERT: B 263 MET cc_start: 0.7989 (ttp) cc_final: 0.7522 (tpp) REVERT: B 615 LEU cc_start: 0.9084 (tt) cc_final: 0.8589 (mm) REVERT: B 709 MET cc_start: 0.9089 (mtp) cc_final: 0.8841 (mtp) REVERT: B 762 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 930 LEU cc_start: 0.9685 (mt) cc_final: 0.9441 (mp) REVERT: B 1011 MET cc_start: 0.9055 (tpp) cc_final: 0.8562 (tpp) REVERT: C 194 LEU cc_start: 0.9406 (tp) cc_final: 0.9148 (mm) REVERT: C 888 PHE cc_start: 0.9434 (m-80) cc_final: 0.9233 (m-80) REVERT: C 932 ASP cc_start: 0.9076 (t0) cc_final: 0.8684 (t0) REVERT: D 462 MET cc_start: 0.4591 (ptp) cc_final: 0.4275 (ptt) REVERT: D 557 MET cc_start: 0.7813 (ppp) cc_final: 0.7505 (ppp) outliers start: 1 outliers final: 1 residues processed: 175 average time/residue: 0.1761 time to fit residues: 49.5027 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 : 0.985 ------------------------------------------------------------------------------- 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: 0.0980 chunk 304 optimal weight: 50.0000 chunk 242 optimal weight: 8.9990 chunk 210 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 186 optimal weight: 0.9980 chunk 251 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 191 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN A 135 ASN A 201 GLN A 984 GLN A 987 GLN A1088 GLN B 135 ASN B 201 GLN B 835 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN B 992 GLN B1005 ASN 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 Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.051382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034459 restraints weight = 272393.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.035473 restraints weight = 171576.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.036053 restraints weight = 124645.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.036477 restraints weight = 100860.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.036752 restraints weight = 87742.987| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28616 Z= 0.190 Angle : 0.666 8.279 39088 Z= 0.336 Chirality : 0.043 0.196 4624 Planarity : 0.004 0.075 4881 Dihedral : 5.192 25.548 3634 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.03 % Allowed : 2.10 % Favored : 97.87 % 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: -2.28 (0.13), residues: 3364 helix: -0.38 (0.16), residues: 982 sheet: -1.38 (0.19), residues: 643 loop : -2.28 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 620 TYR 0.017 0.002 TYR A 886 PHE 0.027 0.002 PHE B 741 TRP 0.026 0.002 TRP D 478 HIS 0.006 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (28485) covalent geometry : angle 0.64625 / 0.33 (38735) SS BOND : bond 0.00350 / 0.21 ( 40) SS BOND : angle 1.26224 / 0.89 ( 80) hydrogen bonds : bond 0.04848 / 3.25 ( 1085) hydrogen bonds : angle 6.07729 / 4.13 ( 3057) link_ALPHA1-3 : bond 0.00339 / 0.22 ( 10) link_ALPHA1-3 : angle 1.67505 / 1.21 ( 30) link_ALPHA1-6 : bond 0.01069 / 0.56 ( 1) link_ALPHA1-6 : angle 2.19840 / 1.24 ( 3) link_BETA1-4 : bond 0.00476 / 0.29 ( 47) link_BETA1-4 : angle 1.76912 / 1.17 ( 141) link_NAG-ASN : bond 0.00411 / 0.30 ( 33) link_NAG-ASN : angle 2.24223 / 1.54 ( 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 141 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 1.064 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: 0.7063 (mmp) cc_final: 0.6657 (mmm) REVERT: A 184 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8176 (mp0) REVERT: A 263 MET cc_start: 0.9016 (ttp) cc_final: 0.8654 (tmm) REVERT: A 264 LEU cc_start: 0.9591 (mt) cc_final: 0.8991 (mt) REVERT: A 1032 MET cc_start: 0.8144 (ttp) cc_final: 0.7914 (ttm) REVERT: B 37 MET cc_start: 0.9189 (mtp) cc_final: 0.8879 (mpp) REVERT: B 188 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8945 (ttpt) REVERT: B 263 MET cc_start: 0.7982 (ttp) cc_final: 0.7620 (tpp) REVERT: B 930 LEU cc_start: 0.9656 (mt) cc_final: 0.9443 (mp) REVERT: B 1011 MET cc_start: 0.9046 (tpp) cc_final: 0.8554 (tpp) REVERT: C 107 MET cc_start: 0.4877 (mmt) cc_final: 0.4581 (mmt) REVERT: C 151 MET cc_start: 0.6209 (mtp) cc_final: 0.5967 (mtp) REVERT: C 194 LEU cc_start: 0.9416 (tp) cc_final: 0.9111 (mm) REVERT: C 932 ASP cc_start: 0.9182 (t0) cc_final: 0.8807 (t0) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.1742 time to fit residues: 40.1166 Evaluate side-chains 107 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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: 7.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 15 optimal weight: 40.0000 chunk 76 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN A 201 GLN A1088 GLN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 759 ASN B 835 GLN B 877 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1030 HIS 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 ** 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 = 0.3478 r_free = 0.3478 target = 0.050588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.033802 restraints weight = 275111.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.034763 restraints weight = 172586.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.035276 restraints weight = 126249.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035713 restraints weight = 103699.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.035985 restraints weight = 90632.698| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 28616 Z= 0.224 Angle : 0.695 9.343 39088 Z= 0.350 Chirality : 0.044 0.228 4624 Planarity : 0.004 0.053 4881 Dihedral : 5.203 25.277 3634 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -2.11 (0.14), residues: 3364 helix: -0.08 (0.16), residues: 975 sheet: -1.32 (0.19), residues: 641 loop : -2.25 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 306 TYR 0.017 0.002 TYR C 53 PHE 0.017 0.002 PHE A 782 TRP 0.014 0.002 TRP D 478 HIS 0.007 0.001 HIS C 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (28485) covalent geometry : angle 0.67773 / 0.35 (38735) SS BOND : bond 0.00467 / 0.26 ( 40) SS BOND : angle 1.28865 / 0.91 ( 80) hydrogen bonds : bond 0.04518 / 3.02 ( 1085) hydrogen bonds : angle 6.04014 / 4.09 ( 3057) link_ALPHA1-3 : bond 0.00330 / 0.21 ( 10) link_ALPHA1-3 : angle 1.76943 / 1.28 ( 30) link_ALPHA1-6 : bond 0.01030 / 0.54 ( 1) link_ALPHA1-6 : angle 2.06490 / 1.17 ( 3) link_BETA1-4 : bond 0.00458 / 0.28 ( 47) link_BETA1-4 : angle 1.71007 / 1.14 ( 141) link_NAG-ASN : bond 0.00488 / 0.35 ( 33) link_NAG-ASN : angle 2.06216 / 1.38 ( 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 130 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.975 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: 0.7124 (mmp) cc_final: 0.6544 (tpp) REVERT: A 184 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8170 (mp0) REVERT: A 263 MET cc_start: 0.9125 (ttp) cc_final: 0.8710 (tmm) REVERT: A 264 LEU cc_start: 0.9597 (mt) cc_final: 0.8977 (mt) REVERT: B 37 MET cc_start: 0.9063 (mtp) cc_final: 0.8700 (mpp) REVERT: B 188 LYS cc_start: 0.9112 (mtmt) cc_final: 0.8821 (ttmt) REVERT: B 263 MET cc_start: 0.8129 (ttp) cc_final: 0.7655 (tpp) REVERT: B 1011 MET cc_start: 0.9094 (tpp) cc_final: 0.8645 (tpp) REVERT: C 107 MET cc_start: 0.5225 (mmt) cc_final: 0.4896 (mmt) REVERT: C 194 LEU cc_start: 0.9446 (tp) cc_final: 0.9103 (mm) REVERT: C 888 PHE cc_start: 0.9377 (m-80) cc_final: 0.9059 (m-80) REVERT: C 932 ASP cc_start: 0.9298 (t0) cc_final: 0.8923 (t0) REVERT: D 462 MET cc_start: 0.4908 (ptt) cc_final: 0.4530 (ptt) REVERT: D 471 ASP cc_start: 0.8670 (t0) cc_final: 0.8446 (p0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1650 time to fit residues: 35.6847 Evaluate side-chains 107 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 30.0000 chunk 257 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 331 optimal weight: 20.0000 chunk 317 optimal weight: 2.9990 chunk 316 optimal weight: 50.0000 chunk 174 optimal weight: 9.9990 chunk 290 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 479 ASN ** B 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 935 ASN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN ** C 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 ASN C 947 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.049014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.032448 restraints weight = 287123.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.033384 restraints weight = 180534.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.033973 restraints weight = 132043.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.034331 restraints weight = 107451.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.034523 restraints weight = 94230.860| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 28616 Z= 0.342 Angle : 0.877 10.874 39088 Z= 0.439 Chirality : 0.047 0.292 4624 Planarity : 0.006 0.126 4881 Dihedral : 5.818 28.858 3634 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -2.41 (0.13), residues: 3364 helix: -0.50 (0.15), residues: 976 sheet: -1.38 (0.20), residues: 607 loop : -2.38 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 99 TYR 0.029 0.003 TYR B 738 PHE 0.028 0.003 PHE A1034 TRP 0.024 0.002 TRP D 271 HIS 0.014 0.002 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00707 / 0.34 (28485) covalent geometry : angle 0.85766 / 0.43 (38735) SS BOND : bond 0.00477 / 0.30 ( 40) SS BOND : angle 1.58237 / 1.11 ( 80) hydrogen bonds : bond 0.04979 / 3.30 ( 1085) hydrogen bonds : angle 6.47478 / 4.39 ( 3057) link_ALPHA1-3 : bond 0.00399 / 0.23 ( 10) link_ALPHA1-3 : angle 2.07517 / 1.53 ( 30) link_ALPHA1-6 : bond 0.01140 / 0.60 ( 1) link_ALPHA1-6 : angle 2.38227 / 1.34 ( 3) link_BETA1-4 : bond 0.00561 / 0.34 ( 47) link_BETA1-4 : angle 1.93911 / 1.29 ( 141) link_NAG-ASN : bond 0.00974 / 0.70 ( 33) link_NAG-ASN : angle 2.65087 / 1.66 ( 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 116 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.9125 (ttp) cc_final: 0.8634 (tmm) REVERT: A 264 LEU cc_start: 0.9580 (mt) cc_final: 0.8973 (mt) REVERT: B 37 MET cc_start: 0.9073 (mtp) cc_final: 0.8685 (mpp) REVERT: B 107 MET cc_start: 0.6946 (mmt) cc_final: 0.6588 (mmt) REVERT: B 263 MET cc_start: 0.8225 (ttp) cc_final: 0.7567 (tpp) REVERT: B 1011 MET cc_start: 0.9190 (tpp) cc_final: 0.8697 (tpp) REVERT: C 107 MET cc_start: 0.5846 (mmt) cc_final: 0.5378 (mmt) REVERT: C 151 MET cc_start: 0.7468 (mtp) cc_final: 0.7182 (mtp) REVERT: C 194 LEU cc_start: 0.9528 (tp) cc_final: 0.9115 (mm) REVERT: C 932 ASP cc_start: 0.9431 (t0) cc_final: 0.9129 (t0) REVERT: C 1011 MET cc_start: 0.9517 (tpp) cc_final: 0.9028 (tpp) REVERT: D 152 MET cc_start: 0.4108 (ptp) cc_final: 0.3754 (ptp) REVERT: D 190 MET cc_start: 0.7313 (mmt) cc_final: 0.7098 (tpp) REVERT: D 462 MET cc_start: 0.4760 (ptt) cc_final: 0.4502 (ptt) REVERT: D 471 ASP cc_start: 0.8597 (t0) cc_final: 0.8383 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1821 time to fit residues: 34.7821 Evaluate side-chains 93 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 1.9990 chunk 153 optimal weight: 9.9990 chunk 168 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 202 optimal weight: 0.2980 chunk 188 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 135 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 993 GLN A1088 GLN B 201 GLN B 381 ASN B 835 GLN B 992 GLN B 993 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 ASN C 917 GLN C 974 GLN C 993 GLN C1088 GLN D 64 ASN ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.051092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.034111 restraints weight = 275580.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035135 restraints weight = 170999.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.035643 restraints weight = 123284.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.036134 restraints weight = 101195.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036344 restraints weight = 88079.027| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28616 Z= 0.124 Angle : 0.638 8.972 39088 Z= 0.318 Chirality : 0.044 0.236 4624 Planarity : 0.004 0.050 4881 Dihedral : 5.181 25.551 3634 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -1.94 (0.14), residues: 3364 helix: 0.25 (0.16), residues: 974 sheet: -1.37 (0.19), residues: 638 loop : -2.21 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 965 TYR 0.020 0.001 TYR D 385 PHE 0.018 0.001 PHE B 262 TRP 0.018 0.001 TRP C 868 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (28485) covalent geometry : angle 0.62166 / 0.31 (38735) SS BOND : bond 0.00368 / 0.21 ( 40) SS BOND : angle 1.36120 / 0.96 ( 80) hydrogen bonds : bond 0.04267 / 2.86 ( 1085) hydrogen bonds : angle 5.76949 / 3.91 ( 3057) link_ALPHA1-3 : bond 0.00472 / 0.31 ( 10) link_ALPHA1-3 : angle 1.56595 / 1.09 ( 30) link_ALPHA1-6 : bond 0.01232 / 0.65 ( 1) link_ALPHA1-6 : angle 1.98320 / 1.11 ( 3) link_BETA1-4 : bond 0.00441 / 0.27 ( 47) link_BETA1-4 : angle 1.57311 / 1.04 ( 141) link_NAG-ASN : bond 0.00283 / 0.20 ( 33) link_NAG-ASN : angle 1.94251 / 1.28 ( 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 133 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.803 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 263 MET cc_start: 0.9119 (ttp) cc_final: 0.8734 (tmm) REVERT: A 264 LEU cc_start: 0.9591 (mt) cc_final: 0.8993 (mt) REVERT: A 722 MET cc_start: 0.8193 (mmm) cc_final: 0.7854 (tmm) REVERT: A 884 MET cc_start: 0.9492 (mmp) cc_final: 0.9168 (mmm) REVERT: A 1009 THR cc_start: 0.9543 (m) cc_final: 0.9339 (t) REVERT: B 37 MET cc_start: 0.8989 (mtp) cc_final: 0.8660 (mpp) REVERT: B 188 LYS cc_start: 0.9029 (mtmt) cc_final: 0.8481 (tttt) REVERT: B 263 MET cc_start: 0.7968 (ttp) cc_final: 0.7514 (tpp) REVERT: B 1011 MET cc_start: 0.9019 (tpp) cc_final: 0.8656 (tpp) REVERT: C 151 MET cc_start: 0.6445 (mtp) cc_final: 0.6121 (mtp) REVERT: C 194 LEU cc_start: 0.9397 (tp) cc_final: 0.9076 (mm) REVERT: C 263 MET cc_start: 0.8781 (mmp) cc_final: 0.8115 (mmm) REVERT: C 932 ASP cc_start: 0.9289 (t0) cc_final: 0.8915 (t0) REVERT: C 1011 MET cc_start: 0.9409 (tpp) cc_final: 0.8798 (tpp) REVERT: D 152 MET cc_start: 0.4266 (ptp) cc_final: 0.3987 (ptp) REVERT: D 190 MET cc_start: 0.7194 (mmt) cc_final: 0.6982 (tpp) REVERT: D 462 MET cc_start: 0.4915 (ptt) cc_final: 0.4585 (ptt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1676 time to fit residues: 37.0936 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 : 0.862 ------------------------------------------------------------------------------- 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: 10.0000 chunk 327 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 264 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 225 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 984 GLN 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** C1088 GLN ** 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 = 0.3468 r_free = 0.3468 target = 0.050291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.033393 restraints weight = 283355.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.034394 restraints weight = 175900.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.035023 restraints weight = 127851.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.035346 restraints weight = 103504.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035656 restraints weight = 90767.169| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28616 Z= 0.187 Angle : 0.661 8.120 39088 Z= 0.330 Chirality : 0.043 0.207 4624 Planarity : 0.004 0.049 4881 Dihedral : 5.101 24.793 3634 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % 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: -1.89 (0.14), residues: 3364 helix: 0.30 (0.16), residues: 978 sheet: -1.24 (0.20), residues: 610 loop : -2.23 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 965 TYR 0.015 0.002 TYR A 886 PHE 0.015 0.002 PHE C 909 TRP 0.016 0.002 TRP A 868 HIS 0.010 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (28485) covalent geometry : angle 0.64428 / 0.33 (38735) SS BOND : bond 0.00377 / 0.23 ( 40) SS BOND : angle 1.28082 / 0.91 ( 80) hydrogen bonds : bond 0.04167 / 2.79 ( 1085) hydrogen bonds : angle 5.81963 / 3.95 ( 3057) link_ALPHA1-3 : bond 0.00317 / 0.21 ( 10) link_ALPHA1-3 : angle 1.69319 / 1.22 ( 30) link_ALPHA1-6 : bond 0.00813 / 0.43 ( 1) link_ALPHA1-6 : angle 1.86261 / 1.05 ( 3) link_BETA1-4 : bond 0.00438 / 0.26 ( 47) link_BETA1-4 : angle 1.63218 / 1.08 ( 141) link_NAG-ASN : bond 0.00468 / 0.33 ( 33) link_NAG-ASN : angle 1.95678 / 1.27 ( 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 125 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.068 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 151 MET cc_start: 0.6961 (tpt) cc_final: 0.6518 (tpt) REVERT: A 263 MET cc_start: 0.9163 (ttp) cc_final: 0.8741 (tmm) REVERT: A 264 LEU cc_start: 0.9589 (mt) cc_final: 0.8968 (mt) REVERT: A 713 MET cc_start: 0.8898 (ttp) cc_final: 0.8623 (tmm) REVERT: A 722 MET cc_start: 0.8327 (mmm) cc_final: 0.7978 (tmm) REVERT: A 770 MET cc_start: 0.8381 (mpp) cc_final: 0.7817 (mpp) REVERT: A 884 MET cc_start: 0.9502 (mmp) cc_final: 0.9197 (mmp) REVERT: B 37 MET cc_start: 0.9074 (mtp) cc_final: 0.8702 (mpp) REVERT: B 107 MET cc_start: 0.6923 (mmt) cc_final: 0.6616 (mmt) REVERT: B 188 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8564 (tttt) REVERT: B 263 MET cc_start: 0.8076 (ttp) cc_final: 0.7577 (tpp) REVERT: B 713 MET cc_start: 0.9028 (tpp) cc_final: 0.8825 (tpt) REVERT: B 882 MET cc_start: 0.9329 (mtp) cc_final: 0.9126 (mtt) REVERT: B 1011 MET cc_start: 0.9101 (tpp) cc_final: 0.8652 (tpp) REVERT: C 194 LEU cc_start: 0.9439 (tp) cc_final: 0.8970 (mp) REVERT: C 263 MET cc_start: 0.8742 (mmp) cc_final: 0.8376 (mmm) REVERT: C 679 MET cc_start: 0.8888 (tpp) cc_final: 0.8591 (tpp) REVERT: C 888 PHE cc_start: 0.9394 (m-80) cc_final: 0.9102 (m-80) REVERT: C 932 ASP cc_start: 0.9318 (t0) cc_final: 0.8957 (t0) REVERT: C 1011 MET cc_start: 0.9460 (tpp) cc_final: 0.9064 (tpp) REVERT: D 152 MET cc_start: 0.4552 (ptp) cc_final: 0.4049 (ptp) REVERT: D 190 MET cc_start: 0.7156 (mmt) cc_final: 0.6949 (tpp) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1607 time to fit residues: 33.6450 Evaluate side-chains 99 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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: 8.9990 chunk 128 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 293 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 268 optimal weight: 0.0770 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 201 GLN B 835 GLN B 939 GLN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 GLN ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN ** D 373 HIS ** 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 = 0.3498 r_free = 0.3498 target = 0.051203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.034138 restraints weight = 268619.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.035146 restraints weight = 165275.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035714 restraints weight = 119012.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.036198 restraints weight = 96301.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.036421 restraints weight = 83120.792| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 28616 Z= 0.115 Angle : 0.619 10.550 39088 Z= 0.305 Chirality : 0.042 0.185 4624 Planarity : 0.004 0.049 4881 Dihedral : 4.863 23.575 3634 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % 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: -1.60 (0.14), residues: 3364 helix: 0.61 (0.17), residues: 975 sheet: -1.12 (0.20), residues: 606 loop : -2.07 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1021 TYR 0.015 0.001 TYR D 50 PHE 0.016 0.001 PHE D 369 TRP 0.031 0.002 TRP B 868 HIS 0.004 0.001 HIS D 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (28485) covalent geometry : angle 0.60258 / 0.30 (38735) SS BOND : bond 0.00314 / 0.18 ( 40) SS BOND : angle 1.05934 / 0.75 ( 80) hydrogen bonds : bond 0.03940 / 2.66 ( 1085) hydrogen bonds : angle 5.53009 / 3.76 ( 3057) link_ALPHA1-3 : bond 0.00441 / 0.29 ( 10) link_ALPHA1-3 : angle 1.52210 / 1.07 ( 30) link_ALPHA1-6 : bond 0.00896 / 0.47 ( 1) link_ALPHA1-6 : angle 1.78329 / 1.00 ( 3) link_BETA1-4 : bond 0.00442 / 0.28 ( 47) link_BETA1-4 : angle 1.52496 / 1.02 ( 141) link_NAG-ASN : bond 0.00243 / 0.17 ( 33) link_NAG-ASN : angle 1.99912 / 1.37 ( 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 130 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.797 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 263 MET cc_start: 0.9277 (ttp) cc_final: 0.8771 (tmm) REVERT: A 264 LEU cc_start: 0.9642 (mt) cc_final: 0.9031 (mt) REVERT: A 679 MET cc_start: 0.9006 (mmp) cc_final: 0.8424 (mmt) REVERT: A 713 MET cc_start: 0.8882 (ttp) cc_final: 0.8516 (tmm) REVERT: A 722 MET cc_start: 0.8435 (mmm) cc_final: 0.8044 (tmm) REVERT: A 770 MET cc_start: 0.8430 (mpp) cc_final: 0.7985 (mpp) REVERT: A 884 MET cc_start: 0.9630 (mmp) cc_final: 0.9238 (mmp) REVERT: A 886 TYR cc_start: 0.9076 (t80) cc_final: 0.8817 (t80) REVERT: A 984 GLN cc_start: 0.9245 (mm110) cc_final: 0.8994 (tp40) REVERT: A 1011 MET cc_start: 0.9183 (tmm) cc_final: 0.8949 (tmm) REVERT: B 37 MET cc_start: 0.9138 (mtp) cc_final: 0.8768 (mpp) REVERT: B 107 MET cc_start: 0.7118 (mmt) cc_final: 0.6849 (mmt) REVERT: B 188 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8471 (mtpt) REVERT: B 263 MET cc_start: 0.8112 (ttp) cc_final: 0.7595 (tpp) REVERT: B 713 MET cc_start: 0.9041 (tpp) cc_final: 0.8820 (tpt) REVERT: B 1011 MET cc_start: 0.9309 (tpp) cc_final: 0.8878 (tpp) REVERT: C 194 LEU cc_start: 0.9464 (tp) cc_final: 0.9137 (mm) REVERT: C 258 LYS cc_start: 0.9264 (mptt) cc_final: 0.8946 (mmtt) REVERT: C 263 MET cc_start: 0.8708 (mmp) cc_final: 0.8281 (mmm) REVERT: C 679 MET cc_start: 0.8953 (tpp) cc_final: 0.8746 (tpp) REVERT: C 758 ARG cc_start: 0.8886 (mmp80) cc_final: 0.8297 (mmp80) REVERT: C 888 PHE cc_start: 0.9527 (m-80) cc_final: 0.9199 (m-80) REVERT: C 932 ASP cc_start: 0.9345 (t0) cc_final: 0.8974 (t0) REVERT: C 1011 MET cc_start: 0.9546 (tpp) cc_final: 0.9236 (tpp) REVERT: D 190 MET cc_start: 0.7168 (mmt) cc_final: 0.6954 (tpp) REVERT: D 462 MET cc_start: 0.5076 (ptt) cc_final: 0.4785 (ptt) REVERT: D 474 MET cc_start: 0.4535 (tpp) cc_final: 0.4259 (tpt) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1659 time to fit residues: 35.5982 Evaluate side-chains 106 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 308 optimal weight: 40.0000 chunk 243 optimal weight: 0.9990 chunk 284 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.050388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.033578 restraints weight = 288770.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.034615 restraints weight = 178937.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.035232 restraints weight = 129229.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.035577 restraints weight = 104280.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.035858 restraints weight = 91539.033| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28616 Z= 0.188 Angle : 0.665 9.745 39088 Z= 0.331 Chirality : 0.043 0.195 4624 Planarity : 0.004 0.048 4881 Dihedral : 4.922 23.569 3634 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % 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: -1.66 (0.14), residues: 3364 helix: 0.48 (0.16), residues: 979 sheet: -1.12 (0.20), residues: 615 loop : -2.07 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 342 TYR 0.026 0.002 TYR D 50 PHE 0.019 0.002 PHE D 315 TRP 0.017 0.002 TRP B 340 HIS 0.007 0.001 HIS C1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (28485) covalent geometry : angle 0.64824 / 0.33 (38735) SS BOND : bond 0.00556 / 0.35 ( 40) SS BOND : angle 1.57093 / 1.14 ( 80) hydrogen bonds : bond 0.03975 / 2.67 ( 1085) hydrogen bonds : angle 5.69302 / 3.86 ( 3057) link_ALPHA1-3 : bond 0.00318 / 0.21 ( 10) link_ALPHA1-3 : angle 1.65960 / 1.20 ( 30) link_ALPHA1-6 : bond 0.01178 / 0.62 ( 1) link_ALPHA1-6 : angle 2.02688 / 1.13 ( 3) link_BETA1-4 : bond 0.00458 / 0.28 ( 47) link_BETA1-4 : angle 1.60205 / 1.06 ( 141) link_NAG-ASN : bond 0.00448 / 0.32 ( 33) link_NAG-ASN : angle 1.96059 / 1.31 ( 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 117 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.110 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: 0.6903 (tpt) cc_final: 0.6528 (tpt) REVERT: A 263 MET cc_start: 0.9298 (ttp) cc_final: 0.8715 (tmm) REVERT: A 264 LEU cc_start: 0.9638 (mt) cc_final: 0.9003 (mt) REVERT: A 722 MET cc_start: 0.8568 (mmm) cc_final: 0.8153 (tmm) REVERT: A 770 MET cc_start: 0.8470 (mpp) cc_final: 0.7940 (mpp) REVERT: A 884 MET cc_start: 0.9624 (mmp) cc_final: 0.9239 (mmp) REVERT: A 886 TYR cc_start: 0.9142 (t80) cc_final: 0.8842 (t80) REVERT: A 1011 MET cc_start: 0.9170 (tmm) cc_final: 0.8922 (tmm) REVERT: B 37 MET cc_start: 0.9205 (mtp) cc_final: 0.8822 (mpp) REVERT: B 107 MET cc_start: 0.7090 (mmt) cc_final: 0.6818 (mmt) REVERT: B 188 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8503 (mtpt) REVERT: B 263 MET cc_start: 0.8212 (ttp) cc_final: 0.7681 (tpp) REVERT: B 713 MET cc_start: 0.9097 (tpp) cc_final: 0.8863 (tpt) REVERT: B 851 MET cc_start: 0.9417 (mtm) cc_final: 0.9199 (mtt) REVERT: B 882 MET cc_start: 0.9474 (mtp) cc_final: 0.9211 (mtt) REVERT: B 1011 MET cc_start: 0.9306 (tpp) cc_final: 0.8835 (tpp) REVERT: C 151 MET cc_start: 0.6532 (mtp) cc_final: 0.6260 (mtp) REVERT: C 194 LEU cc_start: 0.9504 (tp) cc_final: 0.9130 (mm) REVERT: C 258 LYS cc_start: 0.9319 (mptt) cc_final: 0.8982 (mmtt) REVERT: C 263 MET cc_start: 0.8813 (mmp) cc_final: 0.8472 (mmm) REVERT: C 932 ASP cc_start: 0.9406 (t0) cc_final: 0.9058 (t0) REVERT: C 1011 MET cc_start: 0.9581 (tpp) cc_final: 0.9269 (tpp) REVERT: D 462 MET cc_start: 0.5341 (ptt) cc_final: 0.5082 (ptt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1742 time to fit residues: 33.9786 Evaluate side-chains 97 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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: 1.9990 chunk 232 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 300 optimal weight: 30.0000 chunk 175 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 201 GLN B 835 GLN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1030 HIS ** C1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.050836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.033976 restraints weight = 273263.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.034964 restraints weight = 170381.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.035596 restraints weight = 123570.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.035924 restraints weight = 99512.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.036189 restraints weight = 87020.462| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28616 Z= 0.133 Angle : 0.621 12.626 39088 Z= 0.308 Chirality : 0.042 0.184 4624 Planarity : 0.004 0.044 4881 Dihedral : 4.794 23.078 3634 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -1.52 (0.14), residues: 3364 helix: 0.66 (0.17), residues: 973 sheet: -1.07 (0.20), residues: 609 loop : -2.00 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 761 TYR 0.018 0.001 TYR D 50 PHE 0.016 0.001 PHE D 356 TRP 0.022 0.002 TRP B 868 HIS 0.005 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (28485) covalent geometry : angle 0.60606 / 0.30 (38735) SS BOND : bond 0.00322 / 0.19 ( 40) SS BOND : angle 1.35669 / 0.99 ( 80) hydrogen bonds : bond 0.03827 / 2.58 ( 1085) hydrogen bonds : angle 5.51336 / 3.73 ( 3057) link_ALPHA1-3 : bond 0.00405 / 0.27 ( 10) link_ALPHA1-3 : angle 1.56060 / 1.11 ( 30) link_ALPHA1-6 : bond 0.00913 / 0.48 ( 1) link_ALPHA1-6 : angle 1.73182 / 0.97 ( 3) link_BETA1-4 : bond 0.00438 / 0.27 ( 47) link_BETA1-4 : angle 1.49767 / 1.00 ( 141) link_NAG-ASN : bond 0.00262 / 0.19 ( 33) link_NAG-ASN : angle 1.79582 / 1.22 ( 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 121 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.074 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: 0.6940 (tpt) cc_final: 0.6714 (tpt) REVERT: A 263 MET cc_start: 0.9187 (ttp) cc_final: 0.8776 (tpp) REVERT: A 264 LEU cc_start: 0.9595 (mt) cc_final: 0.9248 (mt) REVERT: A 722 MET cc_start: 0.8138 (mmm) cc_final: 0.7770 (tmm) REVERT: A 770 MET cc_start: 0.8420 (mpp) cc_final: 0.7995 (mpp) REVERT: A 884 MET cc_start: 0.9511 (mmp) cc_final: 0.9238 (mmp) REVERT: A 886 TYR cc_start: 0.8953 (t80) cc_final: 0.8670 (t80) REVERT: A 984 GLN cc_start: 0.9126 (mm110) cc_final: 0.8840 (tp40) REVERT: B 37 MET cc_start: 0.9009 (mtp) cc_final: 0.8725 (mpp) REVERT: B 107 MET cc_start: 0.6986 (mmt) cc_final: 0.6706 (mmt) REVERT: B 188 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8464 (tttt) REVERT: B 263 MET cc_start: 0.8051 (ttp) cc_final: 0.7636 (tpp) REVERT: B 713 MET cc_start: 0.9011 (tpp) cc_final: 0.8770 (tpt) REVERT: B 1011 MET cc_start: 0.9135 (tpp) cc_final: 0.8742 (tpp) REVERT: C 194 LEU cc_start: 0.9350 (tp) cc_final: 0.9074 (mm) REVERT: C 258 LYS cc_start: 0.9236 (mptt) cc_final: 0.8907 (mmtt) REVERT: C 932 ASP cc_start: 0.9282 (t0) cc_final: 0.8871 (t0) REVERT: C 1011 MET cc_start: 0.9383 (tpp) cc_final: 0.9111 (tpp) REVERT: D 152 MET cc_start: 0.4830 (ptp) cc_final: 0.4534 (ptp) REVERT: D 462 MET cc_start: 0.5078 (ptt) cc_final: 0.4812 (ptt) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1598 time to fit residues: 32.5762 Evaluate side-chains 107 residues out of total 2958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 4.9990 chunk 335 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 329 optimal weight: 5.9990 chunk 338 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 296 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 201 GLN ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 GLN B 201 GLN B 835 GLN B 935 ASN B 992 GLN B1088 GLN ** C 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1030 HIS ** 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 = 0.3488 r_free = 0.3488 target = 0.050803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.034008 restraints weight = 273807.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.035028 restraints weight = 171139.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.035627 restraints weight = 123805.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036003 restraints weight = 99987.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.036221 restraints weight = 87287.395| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28616 Z= 0.134 Angle : 0.623 11.783 39088 Z= 0.307 Chirality : 0.042 0.183 4624 Planarity : 0.004 0.045 4881 Dihedral : 4.686 22.423 3634 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: 0.70 (0.17), residues: 974 sheet: -1.01 (0.20), residues: 613 loop : -1.98 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 758 TYR 0.012 0.001 TYR B 491 PHE 0.016 0.001 PHE C 262 TRP 0.018 0.002 TRP D 271 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (28485) covalent geometry : angle 0.60853 / 0.30 (38735) SS BOND : bond 0.00309 / 0.18 ( 40) SS BOND : angle 1.25137 / 0.90 ( 80) hydrogen bonds : bond 0.03733 / 2.52 ( 1085) hydrogen bonds : angle 5.46184 / 3.70 ( 3057) link_ALPHA1-3 : bond 0.00379 / 0.25 ( 10) link_ALPHA1-3 : angle 1.56433 / 1.12 ( 30) link_ALPHA1-6 : bond 0.00880 / 0.46 ( 1) link_ALPHA1-6 : angle 1.68087 / 0.94 ( 3) link_BETA1-4 : bond 0.00433 / 0.26 ( 47) link_BETA1-4 : angle 1.50086 / 1.00 ( 141) link_NAG-ASN : bond 0.00288 / 0.21 ( 33) link_NAG-ASN : angle 1.75390 / 1.18 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4731.17 seconds wall clock time: 82 minutes 50.48 seconds (4970.48 seconds total)