Starting phenix.real_space_refine on Wed Mar 4 20:44:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.map" model { file = "/net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8s_23235/03_2026/7l8s_23235.cif" } resolution = 4.3 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= 0.003 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 105 5.16 5 C 9978 2.51 5 N 2694 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16057 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3482 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 4 Chain: "D" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "E" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 4 Chain: "F" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.15, per 1000 atoms: 0.26 Number of scatterers: 16057 At special positions: 0 Unit cell: (128.75, 126.69, 144.2, 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 105 16.00 O 3280 8.00 N 2694 7.00 C 9978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.16 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.19 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 601 " - " ASN A 276 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 363 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 137 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 276 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 88 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 289 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 160 " " NAG K 1 " - " ASN C 295 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 160 " " NAG U 1 " - " ASN E 295 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 392 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 295 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 301 " " NAG g 1 " - " ASN A 88 " " NAG h 1 " - " ASN A 241 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 133 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 678.4 milliseconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 34 sheets defined 31.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.822A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.427A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.118A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.391A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 4.013A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.668A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.124A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.974A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.569A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 4.015A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.175A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.518A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.842A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.362A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'L' and resid 24 through 28 Processing helix chain 'L' and resid 48 through 51 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.160A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.668A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 394 through 395 removed outlier: 10.328A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.499A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.499A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.819A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.623A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 301 through 308 removed outlier: 7.071A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.358A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.716A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 426 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 394 through 396 removed outlier: 10.428A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AD3, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.264A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AD5, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK L 99 " --> pdb=" O UNK L 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 62 through 63 removed outlier: 3.921A pdb=" N UNK L 63 " --> pdb=" O UNK L 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK L 70 " --> pdb=" O UNK L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 600 hydrogen bonds defined for protein. 1599 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: 2.65 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3908 1.33 - 1.46: 4881 1.46 - 1.60: 7381 1.60 - 1.74: 28 1.74 - 1.87: 131 Bond restraints: 16329 Sorted by residual: bond pdb=" CB LEU F 661 " pdb=" CG LEU F 661 " ideal model delta sigma weight residual 1.530 1.666 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.65e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.59e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 16324 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 19255 2.48 - 4.96: 2561 4.96 - 7.43: 347 7.43 - 9.91: 42 9.91 - 12.39: 3 Bond angle restraints: 22208 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.91 -8.04 1.04e+00 9.25e-01 5.98e+01 angle pdb=" C TYR C 319 " pdb=" N THR C 320 " pdb=" CA THR C 320 " ideal model delta sigma weight residual 120.63 133.02 -12.39 1.61e+00 3.86e-01 5.92e+01 angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 119.85 127.36 -7.51 1.01e+00 9.80e-01 5.53e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.38e+01 ... (remaining 22203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 10823 21.39 - 42.77: 217 42.77 - 64.16: 62 64.16 - 85.55: 34 85.55 - 106.93: 20 Dihedral angle restraints: 11156 sinusoidal: 5568 harmonic: 5588 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -141.52 55.52 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 145.79 -52.79 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA UNK H 11 " pdb=" C UNK H 11 " pdb=" N UNK H 12 " pdb=" CA UNK H 12 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 11153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1963 0.120 - 0.239: 527 0.239 - 0.359: 232 0.359 - 0.478: 120 0.478 - 0.598: 14 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2853 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG f 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.134 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B 701 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.328 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG i 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3860 2.81 - 3.33: 15336 3.33 - 3.85: 26238 3.85 - 4.38: 31694 4.38 - 4.90: 48832 Nonbonded interactions: 125960 Sorted by model distance: nonbonded pdb=" O3 NAG b 2 " pdb=" O7 NAG b 2 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 276 " pdb=" N ASN E 279 " model vdw 2.322 3.120 nonbonded pdb=" O HIS E 72 " pdb=" ND1 HIS E 72 " model vdw 2.351 3.120 nonbonded pdb=" N ASN A 425 " pdb=" O ASN A 425 " model vdw 2.379 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.405 2.496 ... (remaining 125955 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 33 through 186 or resid 189 through 397 or resid 411 throu \ gh 457 or resid 461 through 505 or resid 601 through 609)) selection = (chain 'C' and (resid 33 through 397 or resid 411 through 505 or resid 602 throu \ gh 610)) selection = (chain 'E' and (resid 33 through 457 or resid 461 through 505 or resid 601 throu \ gh 609)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = chain 'D' selection = (chain 'F' and (resid 520 through 546 or resid 561 through 702)) } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Z' } ncs_group { reference = (chain 'H' and resid 15 through 114) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } 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: 2.150 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.200 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 0.023 0.157 16468 Z= 1.221 Angle : 1.786 20.114 22589 Z= 1.113 Chirality : 0.152 0.598 2856 Planarity : 0.014 0.300 2707 Dihedral : 11.451 106.935 7408 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.20), residues: 1673 helix: 0.66 (0.23), residues: 415 sheet: 0.99 (0.23), residues: 432 loop : 1.09 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 192 TYR 0.054 0.009 TYR B 638 PHE 0.031 0.006 PHE C 383 TRP 0.054 0.009 TRP F 571 HIS 0.011 0.003 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02212 (16329) covalent geometry : angle 1.74136 (22208) SS BOND : bond 0.03571 ( 36) SS BOND : angle 2.63089 ( 72) hydrogen bonds : bond 0.17057 ( 588) hydrogen bonds : angle 7.87198 ( 1599) link_ALPHA1-3 : bond 0.08633 ( 3) link_ALPHA1-3 : angle 5.90086 ( 9) link_ALPHA1-6 : bond 0.05704 ( 3) link_ALPHA1-6 : angle 3.61124 ( 9) link_BETA1-4 : bond 0.07121 ( 32) link_BETA1-4 : angle 4.49639 ( 96) link_NAG-ASN : bond 0.07710 ( 65) link_NAG-ASN : angle 3.04538 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.584 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: C 39 TYR cc_start: 0.8271 (m-80) cc_final: 0.8026 (m-80) REVERT: D 584 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8866 (tm-30) REVERT: D 628 TRP cc_start: 0.7709 (m100) cc_final: 0.7434 (m100) REVERT: D 650 GLN cc_start: 0.8985 (tp40) cc_final: 0.8501 (tm-30) REVERT: D 654 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7560 (tm-30) REVERT: E 39 TYR cc_start: 0.8809 (m-80) cc_final: 0.8484 (m-80) REVERT: E 112 TRP cc_start: 0.8607 (t-100) cc_final: 0.8358 (t-100) REVERT: E 161 MET cc_start: 0.7460 (ppp) cc_final: 0.7027 (ppp) REVERT: E 210 PHE cc_start: 0.8605 (m-80) cc_final: 0.7661 (m-10) REVERT: E 309 ILE cc_start: 0.9395 (pt) cc_final: 0.9048 (tt) REVERT: F 536 THR cc_start: 0.9551 (p) cc_final: 0.9349 (p) REVERT: A 100 MET cc_start: 0.8791 (mtm) cc_final: 0.8553 (mtm) REVERT: A 122 LEU cc_start: 0.9514 (mt) cc_final: 0.9227 (mm) REVERT: A 382 PHE cc_start: 0.9267 (m-80) cc_final: 0.8994 (m-10) REVERT: B 522 PHE cc_start: 0.8449 (t80) cc_final: 0.8183 (t80) REVERT: B 622 ILE cc_start: 0.8721 (mt) cc_final: 0.7789 (mt) REVERT: B 639 THR cc_start: 0.9277 (m) cc_final: 0.8634 (p) REVERT: B 662 GLU cc_start: 0.4533 (mt-10) cc_final: 0.4162 (mt-10) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.1496 time to fit residues: 101.3454 Evaluate side-chains 219 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 300 ASN D 577 GLN D 653 GLN D 658 GLN E 105 HIS E 170 GLN E 300 ASN E 328 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 422 GLN B 575 GLN B 630 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.070936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057389 restraints weight = 71368.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058931 restraints weight = 43171.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060019 restraints weight = 30938.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060659 restraints weight = 24653.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061150 restraints weight = 21446.173| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16468 Z= 0.194 Angle : 0.841 12.167 22589 Z= 0.408 Chirality : 0.050 0.308 2856 Planarity : 0.004 0.039 2707 Dihedral : 9.018 82.575 4163 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 0.26 % Allowed : 2.60 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.20), residues: 1673 helix: 1.18 (0.25), residues: 415 sheet: 0.61 (0.22), residues: 474 loop : 0.47 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 542 TYR 0.029 0.002 TYR E 177 PHE 0.020 0.002 PHE D 522 TRP 0.028 0.002 TRP A 479 HIS 0.006 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00415 (16329) covalent geometry : angle 0.78167 (22208) SS BOND : bond 0.00388 ( 36) SS BOND : angle 1.32411 ( 72) hydrogen bonds : bond 0.06374 ( 588) hydrogen bonds : angle 6.30139 ( 1599) link_ALPHA1-3 : bond 0.00859 ( 3) link_ALPHA1-3 : angle 4.60928 ( 9) link_ALPHA1-6 : bond 0.00797 ( 3) link_ALPHA1-6 : angle 1.85899 ( 9) link_BETA1-4 : bond 0.00647 ( 32) link_BETA1-4 : angle 2.64071 ( 96) link_NAG-ASN : bond 0.00595 ( 65) link_NAG-ASN : angle 2.66031 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 302 time to evaluate : 0.579 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: C 98 ASN cc_start: 0.9170 (t0) cc_final: 0.8766 (t0) REVERT: C 104 MET cc_start: 0.8805 (ttt) cc_final: 0.8548 (ttp) REVERT: C 426 MET cc_start: 0.8613 (tpp) cc_final: 0.8370 (tpp) REVERT: D 522 PHE cc_start: 0.8433 (t80) cc_final: 0.8118 (t80) REVERT: D 523 LEU cc_start: 0.9235 (mt) cc_final: 0.9027 (mt) REVERT: D 530 MET cc_start: 0.7603 (mtp) cc_final: 0.7009 (mtp) REVERT: D 537 LEU cc_start: 0.8516 (mt) cc_final: 0.8080 (mt) REVERT: D 654 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7545 (tm-30) REVERT: E 85 HIS cc_start: 0.7918 (m90) cc_final: 0.7497 (m-70) REVERT: E 112 TRP cc_start: 0.8382 (t-100) cc_final: 0.7945 (t-100) REVERT: E 161 MET cc_start: 0.6874 (ppp) cc_final: 0.6399 (ppp) REVERT: E 210 PHE cc_start: 0.8301 (m-80) cc_final: 0.7790 (m-10) REVERT: E 303 THR cc_start: 0.8449 (p) cc_final: 0.8085 (p) REVERT: E 492 GLU cc_start: 0.8627 (tt0) cc_final: 0.8253 (pm20) REVERT: F 568 ASP cc_start: 0.7868 (t0) cc_final: 0.7621 (t0) REVERT: F 603 ILE cc_start: 0.9337 (mt) cc_final: 0.9023 (mt) REVERT: F 648 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8436 (mm-30) REVERT: A 95 MET cc_start: 0.8983 (ptt) cc_final: 0.7851 (ppp) REVERT: A 109 ILE cc_start: 0.9438 (mt) cc_final: 0.9148 (tt) REVERT: A 122 LEU cc_start: 0.9306 (mt) cc_final: 0.9090 (mm) REVERT: A 382 PHE cc_start: 0.9042 (m-80) cc_final: 0.8757 (m-10) REVERT: A 424 ILE cc_start: 0.9303 (mm) cc_final: 0.9040 (mm) REVERT: B 568 ASP cc_start: 0.7572 (t0) cc_final: 0.7121 (t0) REVERT: B 575 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: B 596 TRP cc_start: 0.9077 (m-10) cc_final: 0.8769 (m-10) outliers start: 4 outliers final: 0 residues processed: 305 average time/residue: 0.1260 time to fit residues: 57.9694 Evaluate side-chains 188 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 166 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 188 optimal weight: 20.0000 chunk 161 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 186 optimal weight: 30.0000 chunk 123 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS D 577 GLN D 607 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 630 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS B 651 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.068480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054583 restraints weight = 73505.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056077 restraints weight = 44566.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057082 restraints weight = 32116.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.057760 restraints weight = 25841.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058158 restraints weight = 22334.136| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16468 Z= 0.224 Angle : 0.777 9.487 22589 Z= 0.380 Chirality : 0.048 0.271 2856 Planarity : 0.004 0.059 2707 Dihedral : 8.077 77.165 4163 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.13 % Allowed : 3.12 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.73 (0.20), residues: 1673 helix: 1.34 (0.26), residues: 415 sheet: 0.46 (0.23), residues: 465 loop : 0.17 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 308 TYR 0.028 0.002 TYR F 638 PHE 0.027 0.002 PHE E 53 TRP 0.027 0.002 TRP E 479 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00489 (16329) covalent geometry : angle 0.73622 (22208) SS BOND : bond 0.00471 ( 36) SS BOND : angle 1.20410 ( 72) hydrogen bonds : bond 0.05336 ( 588) hydrogen bonds : angle 5.94673 ( 1599) link_ALPHA1-3 : bond 0.00619 ( 3) link_ALPHA1-3 : angle 3.63049 ( 9) link_ALPHA1-6 : bond 0.00835 ( 3) link_ALPHA1-6 : angle 1.47237 ( 9) link_BETA1-4 : bond 0.00601 ( 32) link_BETA1-4 : angle 1.89832 ( 96) link_NAG-ASN : bond 0.00620 ( 65) link_NAG-ASN : angle 2.28251 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 0.668 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: C 39 TYR cc_start: 0.7914 (m-10) cc_final: 0.7570 (m-80) REVERT: C 98 ASN cc_start: 0.8974 (t0) cc_final: 0.8653 (t0) REVERT: C 104 MET cc_start: 0.8910 (ttt) cc_final: 0.8684 (ttp) REVERT: C 426 MET cc_start: 0.8870 (tpp) cc_final: 0.8609 (tpp) REVERT: C 427 TRP cc_start: 0.8435 (m100) cc_final: 0.8192 (m100) REVERT: D 647 GLU cc_start: 0.9032 (pp20) cc_final: 0.8742 (pp20) REVERT: D 654 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7651 (tm-30) REVERT: E 85 HIS cc_start: 0.7954 (m90) cc_final: 0.7562 (m-70) REVERT: E 210 PHE cc_start: 0.8431 (m-80) cc_final: 0.8014 (m-10) REVERT: F 568 ASP cc_start: 0.7864 (t0) cc_final: 0.7516 (t0) REVERT: F 603 ILE cc_start: 0.9450 (mt) cc_final: 0.9001 (mp) REVERT: F 657 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8450 (tm-30) REVERT: A 100 MET cc_start: 0.8151 (mtm) cc_final: 0.7836 (mtt) REVERT: A 109 ILE cc_start: 0.9392 (mt) cc_final: 0.9094 (tt) REVERT: A 122 LEU cc_start: 0.9190 (mt) cc_final: 0.8957 (mm) REVERT: A 382 PHE cc_start: 0.9026 (m-80) cc_final: 0.8778 (m-10) REVERT: A 424 ILE cc_start: 0.9378 (mm) cc_final: 0.9157 (mm) REVERT: B 522 PHE cc_start: 0.8261 (t80) cc_final: 0.7812 (t80) REVERT: B 543 ASN cc_start: 0.8949 (t0) cc_final: 0.8692 (t0) REVERT: B 596 TRP cc_start: 0.8938 (m-10) cc_final: 0.8725 (m-10) REVERT: B 647 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8797 (mt-10) outliers start: 2 outliers final: 2 residues processed: 241 average time/residue: 0.1227 time to fit residues: 45.5993 Evaluate side-chains 169 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 67 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 173 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN F 651 ASN A 82 GLN A 85 HIS A 170 GLN B 575 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.067663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.054077 restraints weight = 73745.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.055432 restraints weight = 46241.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.056381 restraints weight = 34121.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.056946 restraints weight = 27835.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.057421 restraints weight = 24513.866| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16468 Z= 0.213 Angle : 0.724 9.652 22589 Z= 0.352 Chirality : 0.047 0.415 2856 Planarity : 0.004 0.053 2707 Dihedral : 7.735 72.021 4163 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.20 % Allowed : 2.41 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.41 (0.20), residues: 1673 helix: 1.31 (0.26), residues: 420 sheet: 0.20 (0.23), residues: 472 loop : -0.14 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 542 TYR 0.019 0.002 TYR E 217 PHE 0.026 0.002 PHE F 522 TRP 0.035 0.002 TRP E 479 HIS 0.006 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00464 (16329) covalent geometry : angle 0.68393 (22208) SS BOND : bond 0.00367 ( 36) SS BOND : angle 1.46636 ( 72) hydrogen bonds : bond 0.04898 ( 588) hydrogen bonds : angle 5.77455 ( 1599) link_ALPHA1-3 : bond 0.00618 ( 3) link_ALPHA1-3 : angle 3.54624 ( 9) link_ALPHA1-6 : bond 0.00913 ( 3) link_ALPHA1-6 : angle 1.30240 ( 9) link_BETA1-4 : bond 0.00487 ( 32) link_BETA1-4 : angle 1.67105 ( 96) link_NAG-ASN : bond 0.00364 ( 65) link_NAG-ASN : angle 2.15642 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 234 time to evaluate : 0.571 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: C 39 TYR cc_start: 0.7803 (m-10) cc_final: 0.7520 (m-80) REVERT: C 98 ASN cc_start: 0.9056 (t0) cc_final: 0.8776 (t0) REVERT: D 537 LEU cc_start: 0.8846 (mt) cc_final: 0.8338 (mt) REVERT: D 577 GLN cc_start: 0.8763 (tt0) cc_final: 0.8480 (tp40) REVERT: D 584 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 647 GLU cc_start: 0.9019 (pp20) cc_final: 0.8692 (pp20) REVERT: D 654 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7803 (tm-30) REVERT: E 85 HIS cc_start: 0.7977 (m90) cc_final: 0.7649 (m90) REVERT: E 210 PHE cc_start: 0.8461 (m-80) cc_final: 0.8018 (m-10) REVERT: F 568 ASP cc_start: 0.7703 (t0) cc_final: 0.7309 (t0) REVERT: F 655 LYS cc_start: 0.8727 (pttm) cc_final: 0.8282 (pttm) REVERT: F 657 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8360 (tm-30) REVERT: A 100 MET cc_start: 0.8009 (mtm) cc_final: 0.7701 (mtm) REVERT: A 109 ILE cc_start: 0.9414 (mt) cc_final: 0.9091 (tt) REVERT: A 122 LEU cc_start: 0.9177 (mt) cc_final: 0.8926 (mm) REVERT: A 256 SER cc_start: 0.8869 (p) cc_final: 0.8650 (t) REVERT: A 382 PHE cc_start: 0.8950 (m-80) cc_final: 0.8735 (m-10) REVERT: A 424 ILE cc_start: 0.9353 (mm) cc_final: 0.9135 (mm) REVERT: B 522 PHE cc_start: 0.8437 (t80) cc_final: 0.8041 (t80) REVERT: B 596 TRP cc_start: 0.8972 (m-10) cc_final: 0.8760 (m-10) REVERT: B 599 SER cc_start: 0.9481 (t) cc_final: 0.9217 (p) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 0.1266 time to fit residues: 45.2177 Evaluate side-chains 169 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 120 optimal weight: 0.0870 chunk 48 optimal weight: 6.9990 chunk 173 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 156 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 103 GLN D 577 GLN D 658 GLN F 543 ASN F 630 GLN A 85 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.070173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056577 restraints weight = 72556.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057993 restraints weight = 45841.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.058964 restraints weight = 33511.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059548 restraints weight = 27363.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.060039 restraints weight = 24023.272| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16468 Z= 0.123 Angle : 0.651 8.975 22589 Z= 0.317 Chirality : 0.045 0.227 2856 Planarity : 0.003 0.033 2707 Dihedral : 6.913 64.493 4163 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.13 % Allowed : 1.24 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.59 (0.20), residues: 1673 helix: 1.44 (0.26), residues: 422 sheet: 0.38 (0.23), residues: 450 loop : -0.07 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 500 TYR 0.016 0.001 TYR F 643 PHE 0.028 0.002 PHE F 522 TRP 0.035 0.002 TRP E 479 HIS 0.004 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00261 (16329) covalent geometry : angle 0.62010 (22208) SS BOND : bond 0.00410 ( 36) SS BOND : angle 1.15533 ( 72) hydrogen bonds : bond 0.04477 ( 588) hydrogen bonds : angle 5.50607 ( 1599) link_ALPHA1-3 : bond 0.00823 ( 3) link_ALPHA1-3 : angle 2.93003 ( 9) link_ALPHA1-6 : bond 0.01026 ( 3) link_ALPHA1-6 : angle 1.21374 ( 9) link_BETA1-4 : bond 0.00542 ( 32) link_BETA1-4 : angle 1.43492 ( 96) link_NAG-ASN : bond 0.00326 ( 65) link_NAG-ASN : angle 1.81793 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 1.021 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: C 39 TYR cc_start: 0.7850 (m-10) cc_final: 0.7533 (m-80) REVERT: C 98 ASN cc_start: 0.8947 (t0) cc_final: 0.8662 (t0) REVERT: C 195 ASN cc_start: 0.8385 (t0) cc_final: 0.8169 (t0) REVERT: C 426 MET cc_start: 0.8764 (tpp) cc_final: 0.8488 (tpp) REVERT: D 536 THR cc_start: 0.8451 (m) cc_final: 0.7749 (t) REVERT: D 537 LEU cc_start: 0.8837 (mt) cc_final: 0.8311 (mt) REVERT: D 584 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7396 (tm-30) REVERT: D 590 GLN cc_start: 0.9049 (mm110) cc_final: 0.8514 (tm-30) REVERT: D 641 ILE cc_start: 0.9221 (mt) cc_final: 0.8861 (tt) REVERT: D 647 GLU cc_start: 0.9028 (pp20) cc_final: 0.8716 (pp20) REVERT: D 654 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7807 (tm-30) REVERT: E 85 HIS cc_start: 0.7991 (m90) cc_final: 0.7613 (m90) REVERT: E 95 MET cc_start: 0.9328 (ptm) cc_final: 0.8345 (ppp) REVERT: E 210 PHE cc_start: 0.8385 (m-80) cc_final: 0.8001 (m-10) REVERT: E 217 TYR cc_start: 0.8513 (m-80) cc_final: 0.8198 (m-80) REVERT: F 568 ASP cc_start: 0.7448 (t0) cc_final: 0.6939 (t0) REVERT: F 655 LYS cc_start: 0.8727 (pttm) cc_final: 0.8286 (pttm) REVERT: F 657 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8443 (tm-30) REVERT: A 100 MET cc_start: 0.8117 (mtm) cc_final: 0.7646 (mtm) REVERT: A 109 ILE cc_start: 0.9399 (mt) cc_final: 0.9054 (tt) REVERT: A 122 LEU cc_start: 0.9236 (mt) cc_final: 0.8997 (mm) REVERT: A 256 SER cc_start: 0.8840 (p) cc_final: 0.8618 (t) REVERT: A 370 GLU cc_start: 0.8553 (mp0) cc_final: 0.8342 (mp0) REVERT: B 647 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8821 (mt-10) outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.1262 time to fit residues: 50.2919 Evaluate side-chains 174 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 69 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS B 625 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.067930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054402 restraints weight = 74051.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055785 restraints weight = 46618.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.056710 restraints weight = 34409.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057124 restraints weight = 28147.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.057686 restraints weight = 25216.741| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16468 Z= 0.216 Angle : 0.705 7.622 22589 Z= 0.346 Chirality : 0.046 0.239 2856 Planarity : 0.004 0.031 2707 Dihedral : 6.981 63.129 4163 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.34 (0.20), residues: 1673 helix: 1.29 (0.26), residues: 422 sheet: 0.13 (0.23), residues: 464 loop : -0.20 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 542 TYR 0.020 0.002 TYR D 638 PHE 0.024 0.002 PHE E 53 TRP 0.039 0.002 TRP F 628 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00474 (16329) covalent geometry : angle 0.67352 (22208) SS BOND : bond 0.00460 ( 36) SS BOND : angle 1.33004 ( 72) hydrogen bonds : bond 0.04641 ( 588) hydrogen bonds : angle 5.61418 ( 1599) link_ALPHA1-3 : bond 0.00727 ( 3) link_ALPHA1-3 : angle 2.79260 ( 9) link_ALPHA1-6 : bond 0.00989 ( 3) link_ALPHA1-6 : angle 1.26224 ( 9) link_BETA1-4 : bond 0.00450 ( 32) link_BETA1-4 : angle 1.54914 ( 96) link_NAG-ASN : bond 0.00350 ( 65) link_NAG-ASN : angle 1.92225 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 0.585 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: C 39 TYR cc_start: 0.8104 (m-10) cc_final: 0.7803 (m-80) REVERT: C 195 ASN cc_start: 0.8606 (t0) cc_final: 0.8310 (t0) REVERT: C 426 MET cc_start: 0.8769 (tpp) cc_final: 0.8523 (tpp) REVERT: D 536 THR cc_start: 0.8623 (m) cc_final: 0.7906 (t) REVERT: D 630 GLN cc_start: 0.8980 (mt0) cc_final: 0.8776 (tp-100) REVERT: D 647 GLU cc_start: 0.9116 (pp20) cc_final: 0.8798 (pp20) REVERT: D 654 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7852 (tm-30) REVERT: E 85 HIS cc_start: 0.8142 (m90) cc_final: 0.7779 (m90) REVERT: E 210 PHE cc_start: 0.8566 (m-80) cc_final: 0.8111 (m-10) REVERT: F 530 MET cc_start: 0.7929 (mpp) cc_final: 0.7436 (mpp) REVERT: F 568 ASP cc_start: 0.7421 (t0) cc_final: 0.6811 (t0) REVERT: F 655 LYS cc_start: 0.8715 (pttm) cc_final: 0.8375 (pttm) REVERT: F 657 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 100 MET cc_start: 0.8213 (mtm) cc_final: 0.7675 (mtt) REVERT: A 109 ILE cc_start: 0.9424 (mt) cc_final: 0.9102 (tt) REVERT: A 122 LEU cc_start: 0.9314 (mt) cc_final: 0.9045 (mm) REVERT: A 256 SER cc_start: 0.8865 (p) cc_final: 0.8586 (t) REVERT: B 584 GLU cc_start: 0.8819 (pt0) cc_final: 0.8385 (tm-30) REVERT: B 599 SER cc_start: 0.9519 (t) cc_final: 0.9230 (p) REVERT: B 626 MET cc_start: 0.7966 (mpp) cc_final: 0.7463 (mpp) REVERT: B 646 LEU cc_start: 0.9570 (mt) cc_final: 0.9361 (mt) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.1322 time to fit residues: 43.8678 Evaluate side-chains 158 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 28 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 150 optimal weight: 7.9990 chunk 5 optimal weight: 0.0370 chunk 13 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS C 170 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 328 GLN F 630 GLN A 85 HIS B 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054487 restraints weight = 73013.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.055884 restraints weight = 46141.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056800 restraints weight = 33782.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057390 restraints weight = 27584.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.057578 restraints weight = 24360.826| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16468 Z= 0.161 Angle : 0.657 8.912 22589 Z= 0.321 Chirality : 0.045 0.230 2856 Planarity : 0.003 0.052 2707 Dihedral : 6.648 58.147 4163 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.07 % Allowed : 1.43 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.29 (0.20), residues: 1673 helix: 1.26 (0.26), residues: 424 sheet: 0.11 (0.23), residues: 463 loop : -0.24 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 579 TYR 0.015 0.001 TYR D 638 PHE 0.019 0.002 PHE E 53 TRP 0.024 0.002 TRP F 596 HIS 0.005 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00354 (16329) covalent geometry : angle 0.62776 (22208) SS BOND : bond 0.00436 ( 36) SS BOND : angle 1.26359 ( 72) hydrogen bonds : bond 0.04432 ( 588) hydrogen bonds : angle 5.47835 ( 1599) link_ALPHA1-3 : bond 0.00894 ( 3) link_ALPHA1-3 : angle 2.43645 ( 9) link_ALPHA1-6 : bond 0.01020 ( 3) link_ALPHA1-6 : angle 1.29532 ( 9) link_BETA1-4 : bond 0.00458 ( 32) link_BETA1-4 : angle 1.36621 ( 96) link_NAG-ASN : bond 0.00301 ( 65) link_NAG-ASN : angle 1.81194 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 233 time to evaluate : 0.554 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: C 39 TYR cc_start: 0.8040 (m-10) cc_final: 0.7716 (m-80) REVERT: C 195 ASN cc_start: 0.8535 (t0) cc_final: 0.8220 (t0) REVERT: C 426 MET cc_start: 0.8805 (tpp) cc_final: 0.8527 (tpp) REVERT: D 536 THR cc_start: 0.8588 (m) cc_final: 0.7912 (t) REVERT: D 584 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 647 GLU cc_start: 0.9115 (pp20) cc_final: 0.8822 (pp20) REVERT: D 654 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7843 (tm-30) REVERT: E 85 HIS cc_start: 0.8177 (m90) cc_final: 0.7864 (m90) REVERT: E 95 MET cc_start: 0.9380 (ptm) cc_final: 0.8404 (ppp) REVERT: E 104 MET cc_start: 0.8952 (mmm) cc_final: 0.8214 (tpt) REVERT: E 210 PHE cc_start: 0.8635 (m-80) cc_final: 0.8159 (m-10) REVERT: E 217 TYR cc_start: 0.8376 (m-10) cc_final: 0.7480 (m-10) REVERT: F 530 MET cc_start: 0.7963 (mpp) cc_final: 0.7759 (mpp) REVERT: F 655 LYS cc_start: 0.8718 (pttm) cc_final: 0.8368 (pttp) REVERT: F 657 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8424 (tm-30) REVERT: A 100 MET cc_start: 0.8125 (mtm) cc_final: 0.7597 (mtt) REVERT: A 109 ILE cc_start: 0.9417 (mt) cc_final: 0.9096 (tt) REVERT: A 122 LEU cc_start: 0.9300 (mt) cc_final: 0.9021 (mm) REVERT: A 256 SER cc_start: 0.8814 (p) cc_final: 0.8548 (t) REVERT: A 370 GLU cc_start: 0.8598 (mp0) cc_final: 0.8366 (mp0) REVERT: A 382 PHE cc_start: 0.9086 (m-10) cc_final: 0.8871 (m-10) REVERT: B 599 SER cc_start: 0.9527 (t) cc_final: 0.9227 (p) REVERT: B 626 MET cc_start: 0.7507 (mpp) cc_final: 0.7301 (mpp) REVERT: B 646 LEU cc_start: 0.9527 (mt) cc_final: 0.9303 (mt) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.1350 time to fit residues: 47.3094 Evaluate side-chains 166 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 161 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 169 optimal weight: 40.0000 chunk 37 optimal weight: 0.9990 chunk 182 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 162 optimal weight: 0.9980 chunk 187 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 575 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.069192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055328 restraints weight = 73039.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.056810 restraints weight = 45187.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.057773 restraints weight = 32763.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.058405 restraints weight = 26531.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.058855 restraints weight = 23191.936| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16468 Z= 0.123 Angle : 0.632 10.792 22589 Z= 0.308 Chirality : 0.045 0.283 2856 Planarity : 0.003 0.032 2707 Dihedral : 6.255 59.463 4163 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.12 % 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: 0.33 (0.21), residues: 1673 helix: 1.25 (0.26), residues: 422 sheet: 0.16 (0.22), residues: 472 loop : -0.22 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 542 TYR 0.018 0.001 TYR A 217 PHE 0.017 0.002 PHE A 382 TRP 0.036 0.002 TRP E 479 HIS 0.003 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00269 (16329) covalent geometry : angle 0.60101 (22208) SS BOND : bond 0.00350 ( 36) SS BOND : angle 1.31174 ( 72) hydrogen bonds : bond 0.04255 ( 588) hydrogen bonds : angle 5.31850 ( 1599) link_ALPHA1-3 : bond 0.00934 ( 3) link_ALPHA1-3 : angle 2.13706 ( 9) link_ALPHA1-6 : bond 0.01055 ( 3) link_ALPHA1-6 : angle 1.31929 ( 9) link_BETA1-4 : bond 0.00462 ( 32) link_BETA1-4 : angle 1.26309 ( 96) link_NAG-ASN : bond 0.00292 ( 65) link_NAG-ASN : angle 1.86521 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.085 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: C 39 TYR cc_start: 0.7958 (m-10) cc_final: 0.7626 (m-80) REVERT: C 426 MET cc_start: 0.8847 (tpp) cc_final: 0.8589 (tpp) REVERT: D 536 THR cc_start: 0.8665 (m) cc_final: 0.8031 (t) REVERT: D 584 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8009 (tm-30) REVERT: D 590 GLN cc_start: 0.8902 (mm110) cc_final: 0.8429 (tm-30) REVERT: D 603 ILE cc_start: 0.9068 (mp) cc_final: 0.8681 (mp) REVERT: D 647 GLU cc_start: 0.9071 (pp20) cc_final: 0.8781 (pp20) REVERT: D 654 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7871 (tm-30) REVERT: E 85 HIS cc_start: 0.8072 (m90) cc_final: 0.7754 (m90) REVERT: E 95 MET cc_start: 0.9369 (ptm) cc_final: 0.8453 (ppp) REVERT: E 210 PHE cc_start: 0.8610 (m-80) cc_final: 0.8124 (m-10) REVERT: E 217 TYR cc_start: 0.8341 (m-10) cc_final: 0.7959 (m-10) REVERT: E 381 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8286 (mt-10) REVERT: F 571 TRP cc_start: 0.8509 (t60) cc_final: 0.8052 (t60) REVERT: F 596 TRP cc_start: 0.8450 (m-10) cc_final: 0.8121 (m-10) REVERT: F 655 LYS cc_start: 0.8715 (pttm) cc_final: 0.8381 (pttp) REVERT: F 657 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 100 MET cc_start: 0.8088 (mtm) cc_final: 0.7549 (mtt) REVERT: A 109 ILE cc_start: 0.9396 (mt) cc_final: 0.9037 (tt) REVERT: A 122 LEU cc_start: 0.9271 (mt) cc_final: 0.8985 (mm) REVERT: A 256 SER cc_start: 0.8768 (p) cc_final: 0.8507 (t) REVERT: A 370 GLU cc_start: 0.8583 (mp0) cc_final: 0.8334 (mp0) REVERT: A 382 PHE cc_start: 0.9100 (m-10) cc_final: 0.8696 (m-10) REVERT: B 577 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8699 (tm-30) REVERT: B 599 SER cc_start: 0.9509 (t) cc_final: 0.9219 (p) REVERT: B 646 LEU cc_start: 0.9521 (mt) cc_final: 0.9211 (mt) REVERT: B 654 GLU cc_start: 0.9125 (tt0) cc_final: 0.8438 (tm-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1304 time to fit residues: 46.6099 Evaluate side-chains 168 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 179 optimal weight: 30.0000 chunk 178 optimal weight: 30.0000 chunk 102 optimal weight: 0.0270 chunk 148 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053415 restraints weight = 74396.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054780 restraints weight = 47199.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055638 restraints weight = 34792.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.056233 restraints weight = 28722.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056499 restraints weight = 25332.475| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 16468 Z= 0.253 Angle : 0.727 8.498 22589 Z= 0.356 Chirality : 0.046 0.286 2856 Planarity : 0.004 0.039 2707 Dihedral : 6.781 59.782 4163 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.07 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.06 % 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: 0.07 (0.20), residues: 1673 helix: 1.24 (0.26), residues: 422 sheet: -0.15 (0.23), residues: 457 loop : -0.40 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 542 TYR 0.024 0.002 TYR A 217 PHE 0.023 0.002 PHE E 53 TRP 0.044 0.002 TRP E 479 HIS 0.007 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00557 (16329) covalent geometry : angle 0.69660 (22208) SS BOND : bond 0.00497 ( 36) SS BOND : angle 1.44298 ( 72) hydrogen bonds : bond 0.04565 ( 588) hydrogen bonds : angle 5.59573 ( 1599) link_ALPHA1-3 : bond 0.00716 ( 3) link_ALPHA1-3 : angle 2.35446 ( 9) link_ALPHA1-6 : bond 0.00991 ( 3) link_ALPHA1-6 : angle 1.41496 ( 9) link_BETA1-4 : bond 0.00454 ( 32) link_BETA1-4 : angle 1.40193 ( 96) link_NAG-ASN : bond 0.00347 ( 65) link_NAG-ASN : angle 1.98984 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.578 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: C 39 TYR cc_start: 0.7978 (m-10) cc_final: 0.7646 (m-80) REVERT: C 427 TRP cc_start: 0.8706 (m100) cc_final: 0.8388 (m100) REVERT: D 536 THR cc_start: 0.8714 (m) cc_final: 0.8156 (t) REVERT: D 603 ILE cc_start: 0.9054 (mp) cc_final: 0.8726 (mp) REVERT: D 647 GLU cc_start: 0.9080 (pp20) cc_final: 0.8758 (pp20) REVERT: D 654 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8059 (tm-30) REVERT: E 95 MET cc_start: 0.9350 (ptm) cc_final: 0.8330 (ppp) REVERT: E 210 PHE cc_start: 0.8663 (m-80) cc_final: 0.8316 (m-10) REVERT: A 95 MET cc_start: 0.9231 (ptt) cc_final: 0.8809 (ppp) REVERT: A 100 MET cc_start: 0.8058 (mtm) cc_final: 0.7419 (mtt) REVERT: A 109 ILE cc_start: 0.9399 (mt) cc_final: 0.9042 (tt) REVERT: A 122 LEU cc_start: 0.9266 (mt) cc_final: 0.8966 (mm) REVERT: A 256 SER cc_start: 0.8847 (p) cc_final: 0.8575 (t) REVERT: A 382 PHE cc_start: 0.8965 (m-10) cc_final: 0.8696 (m-10) REVERT: B 577 GLN cc_start: 0.9043 (tm-30) cc_final: 0.8803 (tm-30) REVERT: B 646 LEU cc_start: 0.9526 (mt) cc_final: 0.9301 (mt) REVERT: B 647 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8690 (mp0) REVERT: B 654 GLU cc_start: 0.9153 (tt0) cc_final: 0.8619 (tm-30) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1285 time to fit residues: 42.2543 Evaluate side-chains 144 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 72 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 180 optimal weight: 40.0000 chunk 146 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 155 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.066695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.052974 restraints weight = 74072.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054253 restraints weight = 47963.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.055110 restraints weight = 36089.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.055638 restraints weight = 29984.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.055923 restraints weight = 26736.261| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16468 Z= 0.250 Angle : 0.768 9.028 22589 Z= 0.374 Chirality : 0.047 0.267 2856 Planarity : 0.004 0.033 2707 Dihedral : 7.235 59.343 4163 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.23 (0.20), residues: 1673 helix: 0.87 (0.25), residues: 428 sheet: -0.20 (0.24), residues: 443 loop : -0.60 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.027 0.002 TYR C 217 PHE 0.024 0.002 PHE E 53 TRP 0.067 0.003 TRP F 628 HIS 0.005 0.001 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00549 (16329) covalent geometry : angle 0.73565 (22208) SS BOND : bond 0.00470 ( 36) SS BOND : angle 1.49568 ( 72) hydrogen bonds : bond 0.04825 ( 588) hydrogen bonds : angle 5.81556 ( 1599) link_ALPHA1-3 : bond 0.00724 ( 3) link_ALPHA1-3 : angle 2.22744 ( 9) link_ALPHA1-6 : bond 0.00924 ( 3) link_ALPHA1-6 : angle 1.51611 ( 9) link_BETA1-4 : bond 0.00469 ( 32) link_BETA1-4 : angle 1.38440 ( 96) link_NAG-ASN : bond 0.00473 ( 65) link_NAG-ASN : angle 2.14358 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8105 (m-10) cc_final: 0.7701 (m-80) REVERT: C 427 TRP cc_start: 0.8824 (m100) cc_final: 0.8548 (m100) REVERT: C 484 TYR cc_start: 0.8347 (p90) cc_final: 0.8028 (p90) REVERT: D 536 THR cc_start: 0.8747 (m) cc_final: 0.8181 (t) REVERT: D 647 GLU cc_start: 0.9113 (pp20) cc_final: 0.8807 (pp20) REVERT: D 654 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8288 (tm-30) REVERT: D 657 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8904 (pt0) REVERT: E 95 MET cc_start: 0.9366 (ptm) cc_final: 0.8340 (ppp) REVERT: E 338 TRP cc_start: 0.8901 (t-100) cc_final: 0.8633 (t-100) REVERT: F 643 TYR cc_start: 0.9120 (m-10) cc_final: 0.8807 (m-80) REVERT: A 95 MET cc_start: 0.9300 (ptt) cc_final: 0.8820 (ppp) REVERT: A 100 MET cc_start: 0.8133 (mtm) cc_final: 0.7510 (mtt) REVERT: A 109 ILE cc_start: 0.9345 (mt) cc_final: 0.9048 (tt) REVERT: A 122 LEU cc_start: 0.9273 (mt) cc_final: 0.8984 (mm) REVERT: A 256 SER cc_start: 0.8981 (p) cc_final: 0.8677 (t) REVERT: A 382 PHE cc_start: 0.9141 (m-10) cc_final: 0.8918 (m-10) REVERT: B 577 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8887 (tm-30) REVERT: B 599 SER cc_start: 0.9499 (t) cc_final: 0.9270 (p) REVERT: B 626 MET cc_start: 0.6942 (mpp) cc_final: 0.6424 (mpp) REVERT: B 647 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8708 (mp0) REVERT: B 654 GLU cc_start: 0.9161 (tt0) cc_final: 0.8624 (tm-30) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.1310 time to fit residues: 40.7840 Evaluate side-chains 147 residues out of total 1536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 86 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 112 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.068188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.054140 restraints weight = 73246.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055552 restraints weight = 45902.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056453 restraints weight = 33776.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057075 restraints weight = 27757.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057518 restraints weight = 24459.541| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16468 Z= 0.143 Angle : 0.684 9.040 22589 Z= 0.332 Chirality : 0.046 0.245 2856 Planarity : 0.003 0.034 2707 Dihedral : 6.687 56.935 4163 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.07 % Allowed : 0.20 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.08 (0.20), residues: 1673 helix: 1.00 (0.26), residues: 424 sheet: -0.10 (0.23), residues: 459 loop : -0.51 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 542 TYR 0.021 0.002 TYR E 217 PHE 0.018 0.002 PHE A 382 TRP 0.048 0.002 TRP F 628 HIS 0.003 0.001 HIS D 564 Details of bonding type rmsd covalent geometry : bond 0.00316 (16329) covalent geometry : angle 0.65414 (22208) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.22471 ( 72) hydrogen bonds : bond 0.04431 ( 588) hydrogen bonds : angle 5.58595 ( 1599) link_ALPHA1-3 : bond 0.00880 ( 3) link_ALPHA1-3 : angle 1.92552 ( 9) link_ALPHA1-6 : bond 0.00950 ( 3) link_ALPHA1-6 : angle 1.52774 ( 9) link_BETA1-4 : bond 0.00469 ( 32) link_BETA1-4 : angle 1.25681 ( 96) link_NAG-ASN : bond 0.00441 ( 65) link_NAG-ASN : angle 1.98260 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.06 seconds wall clock time: 42 minutes 36.21 seconds (2556.21 seconds total)