Starting phenix.real_space_refine on Fri Mar 22 13:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vne_32040/03_2024/7vne_32040.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4947 atoms to isotropic. 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 129 5.16 5 C 18224 2.51 5 N 4711 2.21 5 O 5651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 994": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28715 Number of models: 1 Model: "" Number of chains: 31 Chain: "C" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "W" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "A" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "U" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} Chain: "B" Number of atoms: 8372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8372 Classifications: {'peptide': 1070} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1015} Chain breaks: 5 Chain: "V" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 110} 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: 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: "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: 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 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 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 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: "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: 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: 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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.37, per 1000 atoms: 0.54 Number of scatterers: 28715 At special positions: 0 Unit cell: (194.688, 176.436, 162.24, 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 129 16.00 O 5651 8.00 N 4711 7.00 C 18224 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 95 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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 J 2 " - " NAG J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 " - " NAG R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 149 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG B1301 " - " ASN B 343 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 149 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 616 " " NAG C1301 " - " ASN C 343 " " NAG C1302 " - " ASN C 17 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 149 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 616 " " NAG D 1 " - " ASN C 282 " " NAG E 1 " - " ASN C1134 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 801 " " NAG H 1 " - " ASN C1098 " " NAG I 1 " - " ASN C 331 " " NAG J 1 " - " ASN A 165 " " NAG K 1 " - " ASN A 282 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A 331 " " NAG R 1 " - " ASN B 165 " " NAG S 1 " - " ASN B 234 " " NAG T 1 " - " ASN B 282 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN B 709 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B1098 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.29 Conformation dependent library (CDL) restraints added in 5.2 seconds 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6630 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 52 sheets defined 20.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.547A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.513A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.959A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.980A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.835A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.731A pdb=" N MET C 902 " --> pdb=" O PHE C 898 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.756A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.757A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 964 removed outlier: 3.771A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN C 957 " --> pdb=" O ASN C 953 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 965 through 968 removed outlier: 4.062A pdb=" N SER C 968 " --> pdb=" O GLN C 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 965 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.019A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.972A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.101A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 31 Processing helix chain 'W' and resid 101 through 105 removed outlier: 3.978A pdb=" N THR W 104 " --> pdb=" O SER W 101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY W 105 " --> pdb=" O GLY W 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 101 through 105' Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 4.243A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.826A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.090A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.572A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.592A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.919A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.562A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.621A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.524A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.511A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.620A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.708A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.851A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.511A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A1026 " --> pdb=" O ALA A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.071A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 64 removed outlier: 3.594A pdb=" N LYS U 64 " --> pdb=" O PRO U 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 125 removed outlier: 4.416A pdb=" N THR B 124 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN B 125 " --> pdb=" O ASN B 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 121 through 125' Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.525A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 4.332A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 343' Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.573A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.816A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.591A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 783 removed outlier: 3.738A pdb=" N VAL B 772 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 822 Processing helix chain 'B' and resid 866 through 882 removed outlier: 3.603A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.575A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.579A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.563A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.084A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 985 through 1001 removed outlier: 4.180A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1022 removed outlier: 3.554A pdb=" N ILE B1018 " --> pdb=" O ARG B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'V' and resid 27 through 31 removed outlier: 3.567A pdb=" N TYR V 30 " --> pdb=" O SER V 27 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP V 31 " --> pdb=" O SER V 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 27 through 31' Processing helix chain 'V' and resid 60 through 64 removed outlier: 4.024A pdb=" N LYS V 64 " --> pdb=" O PRO V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 90 removed outlier: 3.907A pdb=" N ASP V 89 " --> pdb=" O ARG V 86 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR V 90 " --> pdb=" O ALA V 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 86 through 90' Processing helix chain 'V' and resid 98 through 102 removed outlier: 3.533A pdb=" N SER V 101 " --> pdb=" O ASN V 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.514A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.051A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.149A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.098A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.675A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 197 removed outlier: 6.119A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.931A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.898A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.343A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.563A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 701 through 704 removed outlier: 6.395A pdb=" N ALA C 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LYS A 790 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.952A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AB7, first strand: chain 'C' and resid 787 through 789 removed outlier: 6.093A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'W' and resid 6 through 8 Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.786A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.474A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.908A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.720A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.846A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 378 through 380 removed outlier: 4.340A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG A 509 " --> pdb=" O TRP A 436 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.650A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.752A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.333A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.995A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.995A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.578A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'U' and resid 46 through 51 removed outlier: 6.682A pdb=" N TRP U 36 " --> pdb=" O ILE U 48 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N SER U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N MET U 34 " --> pdb=" O SER U 50 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 67 through 68 removed outlier: 3.573A pdb=" N THR U 68 " --> pdb=" O GLN U 81 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.013A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.313A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.544A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AE3, first strand: chain 'B' and resid 225 through 229 removed outlier: 5.249A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.540A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.540A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AE7, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.965A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 378 through 380 removed outlier: 3.625A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.526A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.135A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 715 through 728 removed outlier: 6.135A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.477A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 3.535A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'V' and resid 5 through 8 removed outlier: 3.508A pdb=" N VAL V 5 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS V 22 " --> pdb=" O LEU V 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU V 78 " --> pdb=" O CYS V 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 91 through 92 removed outlier: 4.207A pdb=" N ALA V 91 " --> pdb=" O VAL V 114 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2073 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: 11.88 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4642 1.31 - 1.44: 8083 1.44 - 1.57: 16464 1.57 - 1.70: 0 1.70 - 1.83: 168 Bond restraints: 29357 Sorted by residual: bond pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 1.346 1.487 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C7 NAG L 2 " pdb=" N2 NAG L 2 " ideal model delta sigma weight residual 1.346 1.484 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C7 NAG X 2 " pdb=" N2 NAG X 2 " ideal model delta sigma weight residual 1.346 1.481 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C7 NAG T 1 " pdb=" N2 NAG T 1 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" C7 NAG C1307 " pdb=" N2 NAG C1307 " ideal model delta sigma weight residual 1.346 1.480 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 29352 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.35: 660 106.35 - 113.32: 16311 113.32 - 120.28: 10351 120.28 - 127.25: 12360 127.25 - 134.22: 261 Bond angle restraints: 39943 Sorted by residual: angle pdb=" N GLN B 580 " pdb=" CA GLN B 580 " pdb=" C GLN B 580 " ideal model delta sigma weight residual 113.43 107.82 5.61 1.26e+00 6.30e-01 1.98e+01 angle pdb=" C PRO B 330 " pdb=" N ASN B 331 " pdb=" CA ASN B 331 " ideal model delta sigma weight residual 120.28 126.23 -5.95 1.44e+00 4.82e-01 1.71e+01 angle pdb=" N TYR C1067 " pdb=" CA TYR C1067 " pdb=" C TYR C1067 " ideal model delta sigma weight residual 109.59 115.74 -6.15 1.61e+00 3.86e-01 1.46e+01 angle pdb=" C8 NAG D 1 " pdb=" C7 NAG D 1 " pdb=" N2 NAG D 1 " ideal model delta sigma weight residual 115.06 126.30 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N TYR B1067 " pdb=" CA TYR B1067 " pdb=" C TYR B1067 " ideal model delta sigma weight residual 109.59 114.95 -5.36 1.61e+00 3.86e-01 1.11e+01 ... (remaining 39938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.25: 17056 25.25 - 50.51: 946 50.51 - 75.76: 159 75.76 - 101.01: 58 101.01 - 126.27: 45 Dihedral angle restraints: 18264 sinusoidal: 7932 harmonic: 10332 Sorted by residual: dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -157.85 71.85 1 1.00e+01 1.00e-02 6.61e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -18.63 -67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -20.72 -65.28 1 1.00e+01 1.00e-02 5.59e+01 ... (remaining 18261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4358 0.099 - 0.198: 309 0.198 - 0.298: 18 0.298 - 0.397: 5 0.397 - 0.496: 1 Chirality restraints: 4691 Sorted by residual: chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.15e+00 chirality pdb=" C2 NAG T 1 " pdb=" C1 NAG T 1 " pdb=" C3 NAG T 1 " pdb=" N2 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.12 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 4688 not shown) Planarity restraints: 5126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1067 " -0.041 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR C1067 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR C1067 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C1067 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR C1067 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C1067 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C1067 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C1067 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1067 " -0.039 2.00e-02 2.50e+03 2.90e-02 1.68e+01 pdb=" CG TYR B1067 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B1067 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B1067 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B1067 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B1067 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B1067 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1067 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 741 " 0.028 2.00e-02 2.50e+03 2.26e-02 1.02e+01 pdb=" CG TYR B 741 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 741 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 741 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 741 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 741 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 741 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 741 " 0.001 2.00e-02 2.50e+03 ... (remaining 5123 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 403 2.65 - 3.21: 26017 3.21 - 3.77: 40464 3.77 - 4.34: 57377 4.34 - 4.90: 93697 Nonbonded interactions: 217958 Sorted by model distance: nonbonded pdb=" OG SER B 673 " pdb=" OH TYR B 695 " model vdw 2.083 2.440 nonbonded pdb=" OE1 GLN B 134 " pdb=" OG SER B 161 " model vdw 2.118 2.440 nonbonded pdb=" O ARG C 214 " pdb=" OH TYR C 266 " model vdw 2.129 2.440 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.178 2.440 nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.185 2.440 ... (remaining 217953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 1146 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'J' selection = chain 'R' } ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.020 Extract box with map and model: 5.570 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 76.190 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 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 : 0.011 0.141 29357 Z= 0.725 Angle : 0.901 11.240 39943 Z= 0.418 Chirality : 0.055 0.496 4691 Planarity : 0.005 0.066 5083 Dihedral : 17.642 126.268 11562 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.13), residues: 3516 helix: -2.21 (0.18), residues: 604 sheet: -0.52 (0.22), residues: 593 loop : -2.14 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 886 HIS 0.011 0.001 HIS B1058 PHE 0.039 0.002 PHE A 906 TYR 0.077 0.002 TYR C1067 ARG 0.006 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 PHE cc_start: 0.6849 (m-80) cc_final: 0.6563 (m-80) REVERT: B 902 MET cc_start: 0.8478 (mmm) cc_final: 0.8218 (mmt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.3720 time to fit residues: 125.9655 Evaluate side-chains 175 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 9.9990 chunk 268 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 277 optimal weight: 40.0000 chunk 107 optimal weight: 50.0000 chunk 168 optimal weight: 0.4980 chunk 206 optimal weight: 0.3980 chunk 321 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 762 GLN C 856 ASN C 955 ASN C 965 GLN C1005 GLN A 81 ASN A 115 GLN A 675 GLN B 474 GLN B 655 HIS B1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29357 Z= 0.207 Angle : 0.697 12.694 39943 Z= 0.332 Chirality : 0.050 0.400 4691 Planarity : 0.004 0.048 5083 Dihedral : 15.877 117.191 5232 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.45 % Allowed : 4.94 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3516 helix: -1.09 (0.19), residues: 645 sheet: -0.42 (0.21), residues: 636 loop : -2.13 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP W 47 HIS 0.005 0.001 HIS A 69 PHE 0.026 0.001 PHE A 238 TYR 0.027 0.001 TYR C1067 ARG 0.006 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: W 47 TRP cc_start: 0.4341 (p-90) cc_final: 0.4045 (p-90) REVERT: A 957 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8568 (tt0) REVERT: A 1002 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8628 (tm-30) REVERT: B 106 PHE cc_start: 0.6799 (m-80) cc_final: 0.6530 (m-80) REVERT: B 990 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (tp30) outliers start: 14 outliers final: 7 residues processed: 212 average time/residue: 0.3696 time to fit residues: 130.6254 Evaluate side-chains 183 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 175 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain U residue 47 TRP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 990 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 218 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 322 optimal weight: 0.5980 chunk 347 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 319 optimal weight: 0.8980 chunk 109 optimal weight: 30.0000 chunk 258 optimal weight: 6.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 965 GLN A 81 ASN A 354 ASN A1135 ASN B 474 GLN B1048 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29357 Z= 0.289 Angle : 0.698 11.592 39943 Z= 0.330 Chirality : 0.051 0.502 4691 Planarity : 0.004 0.046 5083 Dihedral : 15.080 117.081 5232 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.97 % Allowed : 8.62 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3516 helix: -0.66 (0.20), residues: 632 sheet: -0.53 (0.21), residues: 654 loop : -2.10 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 886 HIS 0.008 0.001 HIS B1058 PHE 0.024 0.002 PHE A 238 TYR 0.032 0.001 TYR B 741 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5502 (tt0) cc_final: 0.5194 (tt0) REVERT: C 226 LEU cc_start: 0.7643 (mp) cc_final: 0.7372 (mt) REVERT: W 47 TRP cc_start: 0.4578 (p-90) cc_final: 0.4301 (p-90) REVERT: A 957 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8543 (tt0) REVERT: A 1002 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8611 (tm-30) REVERT: B 106 PHE cc_start: 0.6875 (m-80) cc_final: 0.6541 (m-80) REVERT: B 990 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7882 (tp30) outliers start: 30 outliers final: 17 residues processed: 204 average time/residue: 0.3754 time to fit residues: 127.9729 Evaluate side-chains 200 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 182 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 2.9990 chunk 242 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 153 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 323 optimal weight: 5.9990 chunk 342 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 306 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29357 Z= 0.232 Angle : 0.665 10.196 39943 Z= 0.311 Chirality : 0.049 0.434 4691 Planarity : 0.004 0.126 5083 Dihedral : 14.280 115.600 5232 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 1.29 % Allowed : 10.56 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3516 helix: -0.38 (0.21), residues: 628 sheet: -0.52 (0.21), residues: 651 loop : -2.07 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 258 HIS 0.004 0.001 HIS A 69 PHE 0.037 0.001 PHE A 238 TYR 0.025 0.001 TYR B 741 ARG 0.018 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 193 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5411 (tt0) cc_final: 0.4866 (tt0) REVERT: C 226 LEU cc_start: 0.7565 (mp) cc_final: 0.7260 (mt) REVERT: W 47 TRP cc_start: 0.4714 (p-90) cc_final: 0.4439 (p-90) REVERT: A 81 ASN cc_start: 0.7570 (p0) cc_final: 0.7368 (p0) REVERT: A 957 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8521 (tt0) REVERT: A 1002 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8531 (tm-30) REVERT: B 106 PHE cc_start: 0.6916 (m-80) cc_final: 0.6601 (m-80) REVERT: B 741 TYR cc_start: 0.6606 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: B 990 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7808 (tp30) outliers start: 40 outliers final: 21 residues processed: 222 average time/residue: 0.3548 time to fit residues: 131.9920 Evaluate side-chains 201 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 236 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 955 ASN A 81 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN A1106 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 913 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 29357 Z= 0.443 Angle : 0.767 10.937 39943 Z= 0.366 Chirality : 0.053 0.516 4691 Planarity : 0.005 0.063 5083 Dihedral : 14.118 119.052 5232 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 2.33 % Allowed : 12.47 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3516 helix: -0.72 (0.20), residues: 624 sheet: -0.61 (0.20), residues: 682 loop : -2.20 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 886 HIS 0.009 0.002 HIS B1058 PHE 0.037 0.002 PHE A 238 TYR 0.044 0.002 TYR B 741 ARG 0.012 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 178 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5719 (tt0) cc_final: 0.5519 (tt0) REVERT: C 226 LEU cc_start: 0.7813 (mp) cc_final: 0.7524 (mt) REVERT: C 984 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6920 (mp) REVERT: A 153 MET cc_start: 0.2381 (ppp) cc_final: 0.1948 (ptt) REVERT: A 957 GLN cc_start: 0.8969 (tm-30) cc_final: 0.8534 (tt0) REVERT: A 1036 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: B 741 TYR cc_start: 0.7441 (OUTLIER) cc_final: 0.6078 (m-80) REVERT: B 858 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 990 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7740 (tp30) outliers start: 72 outliers final: 46 residues processed: 232 average time/residue: 0.3566 time to fit residues: 141.3715 Evaluate side-chains 223 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 0.0980 chunk 308 optimal weight: 1.9990 chunk 67 optimal weight: 0.0470 chunk 200 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 342 optimal weight: 0.3980 chunk 284 optimal weight: 40.0000 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN A 493 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29357 Z= 0.169 Angle : 0.643 11.027 39943 Z= 0.302 Chirality : 0.048 0.417 4691 Planarity : 0.004 0.047 5083 Dihedral : 13.243 113.143 5232 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.26 % Allowed : 13.44 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.14), residues: 3516 helix: -0.20 (0.21), residues: 627 sheet: -0.44 (0.21), residues: 634 loop : -2.06 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP W 47 HIS 0.004 0.000 HIS A 69 PHE 0.024 0.001 PHE A 238 TYR 0.026 0.001 TYR C 695 ARG 0.007 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 3.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 191 GLU cc_start: 0.5324 (tt0) cc_final: 0.5056 (tt0) REVERT: C 226 LEU cc_start: 0.7607 (mp) cc_final: 0.7303 (mt) REVERT: C 984 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6894 (mp) REVERT: W 47 TRP cc_start: 0.4754 (p-90) cc_final: 0.4127 (p-90) REVERT: A 153 MET cc_start: 0.2517 (ppp) cc_final: 0.1862 (ptt) REVERT: A 957 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8471 (tt0) REVERT: A 1002 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 1036 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: B 741 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6010 (m-80) REVERT: B 858 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 990 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7770 (tp30) outliers start: 39 outliers final: 17 residues processed: 217 average time/residue: 0.3506 time to fit residues: 128.8736 Evaluate side-chains 200 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 6.9990 chunk 38 optimal weight: 40.0000 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 193 optimal weight: 0.2980 chunk 288 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 341 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29357 Z= 0.292 Angle : 0.688 10.447 39943 Z= 0.323 Chirality : 0.050 0.447 4691 Planarity : 0.004 0.052 5083 Dihedral : 13.084 116.520 5232 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 2.00 % Allowed : 13.57 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.14), residues: 3516 helix: -0.26 (0.21), residues: 627 sheet: -0.38 (0.21), residues: 653 loop : -2.09 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP W 47 HIS 0.009 0.001 HIS B 146 PHE 0.027 0.002 PHE A 238 TYR 0.034 0.001 TYR B 741 ARG 0.006 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 176 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 PHE cc_start: 0.1392 (OUTLIER) cc_final: 0.1115 (m-80) REVERT: C 226 LEU cc_start: 0.7747 (mp) cc_final: 0.7460 (mt) REVERT: C 984 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6930 (mp) REVERT: C 990 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7224 (mt-10) REVERT: W 47 TRP cc_start: 0.5042 (p-90) cc_final: 0.4407 (p-90) REVERT: A 153 MET cc_start: 0.2424 (ppp) cc_final: 0.1910 (ptt) REVERT: A 453 TYR cc_start: 0.1777 (OUTLIER) cc_final: 0.1022 (m-80) REVERT: A 695 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: A 957 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8509 (tt0) REVERT: A 1002 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 1036 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: B 741 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6062 (m-80) REVERT: B 858 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8315 (mt) REVERT: B 990 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7737 (tp30) outliers start: 62 outliers final: 44 residues processed: 226 average time/residue: 0.3576 time to fit residues: 137.0740 Evaluate side-chains 225 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 173 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 901 GLN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1132 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 0.9990 chunk 136 optimal weight: 8.9990 chunk 203 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 268 optimal weight: 0.0970 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS C 955 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29357 Z= 0.171 Angle : 0.632 10.030 39943 Z= 0.295 Chirality : 0.048 0.393 4691 Planarity : 0.004 0.052 5083 Dihedral : 12.477 110.884 5232 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.61 % Allowed : 14.47 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3516 helix: 0.11 (0.21), residues: 622 sheet: -0.33 (0.21), residues: 618 loop : -2.01 (0.13), residues: 2276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP W 47 HIS 0.004 0.001 HIS B 146 PHE 0.018 0.001 PHE A 168 TYR 0.023 0.001 TYR C 695 ARG 0.007 0.000 ARG W 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 190 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 226 LEU cc_start: 0.7598 (mp) cc_final: 0.7380 (mt) REVERT: C 984 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6786 (mp) REVERT: C 990 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7222 (mt-10) REVERT: A 153 MET cc_start: 0.2341 (ppp) cc_final: 0.1835 (ptt) REVERT: A 453 TYR cc_start: 0.1593 (OUTLIER) cc_final: 0.0771 (m-80) REVERT: A 695 TYR cc_start: 0.7101 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: A 957 GLN cc_start: 0.8879 (tm-30) cc_final: 0.8471 (tt0) REVERT: A 1002 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8317 (tm-30) REVERT: A 1036 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8436 (tt0) REVERT: B 423 TYR cc_start: -0.1049 (OUTLIER) cc_final: -0.1322 (m-80) REVERT: B 741 TYR cc_start: 0.6929 (OUTLIER) cc_final: 0.5900 (m-80) REVERT: B 858 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8223 (mt) REVERT: B 954 GLN cc_start: 0.7493 (mt0) cc_final: 0.7191 (mt0) REVERT: B 990 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7712 (tp30) outliers start: 50 outliers final: 29 residues processed: 226 average time/residue: 0.3556 time to fit residues: 135.9501 Evaluate side-chains 215 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 178 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain V residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 0.6980 chunk 326 optimal weight: 0.2980 chunk 298 optimal weight: 0.2980 chunk 317 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 249 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 287 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 316 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1106 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 658 ASN B 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29357 Z= 0.165 Angle : 0.626 10.754 39943 Z= 0.292 Chirality : 0.048 0.369 4691 Planarity : 0.004 0.054 5083 Dihedral : 12.144 109.959 5232 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.49 % Allowed : 14.76 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3516 helix: 0.40 (0.22), residues: 624 sheet: -0.26 (0.21), residues: 634 loop : -1.93 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP W 47 HIS 0.004 0.000 HIS A 69 PHE 0.020 0.001 PHE A 92 TYR 0.022 0.001 TYR C 695 ARG 0.004 0.000 ARG W 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 3.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 990 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7218 (mt-10) REVERT: A 153 MET cc_start: 0.2371 (ppp) cc_final: 0.1819 (ptt) REVERT: A 453 TYR cc_start: 0.1581 (OUTLIER) cc_final: 0.0707 (m-80) REVERT: A 957 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8478 (tt0) REVERT: A 1002 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 1036 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: B 423 TYR cc_start: -0.1072 (OUTLIER) cc_final: -0.1351 (m-80) REVERT: B 741 TYR cc_start: 0.6706 (OUTLIER) cc_final: 0.5782 (m-80) REVERT: B 858 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8218 (mt) REVERT: B 954 GLN cc_start: 0.7510 (mt0) cc_final: 0.7233 (mt0) REVERT: B 990 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7708 (tp30) outliers start: 46 outliers final: 32 residues processed: 222 average time/residue: 0.3510 time to fit residues: 132.5192 Evaluate side-chains 213 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain V residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 2.9990 chunk 336 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 352 optimal weight: 5.9990 chunk 324 optimal weight: 6.9990 chunk 280 optimal weight: 0.0570 chunk 29 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 chunk 172 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29357 Z= 0.225 Angle : 0.642 11.094 39943 Z= 0.300 Chirality : 0.048 0.377 4691 Planarity : 0.004 0.060 5083 Dihedral : 12.062 110.148 5232 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.61 % Allowed : 14.86 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3516 helix: 0.36 (0.21), residues: 622 sheet: -0.20 (0.21), residues: 612 loop : -1.95 (0.13), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP W 47 HIS 0.004 0.001 HIS A1064 PHE 0.041 0.001 PHE A 238 TYR 0.026 0.001 TYR B1067 ARG 0.004 0.000 ARG B 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7032 Ramachandran restraints generated. 3516 Oldfield, 0 Emsley, 3516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 176 time to evaluate : 3.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 PHE cc_start: 0.1446 (OUTLIER) cc_final: 0.1214 (m-80) REVERT: C 277 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8662 (mt) REVERT: A 153 MET cc_start: 0.2287 (ppp) cc_final: 0.1819 (ptt) REVERT: A 453 TYR cc_start: 0.1666 (OUTLIER) cc_final: 0.0796 (m-80) REVERT: A 957 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8476 (tt0) REVERT: A 1002 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8339 (tm-30) REVERT: A 1036 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: B 423 TYR cc_start: -0.1047 (OUTLIER) cc_final: -0.1365 (m-80) REVERT: B 741 TYR cc_start: 0.6816 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: B 858 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8248 (mt) REVERT: B 954 GLN cc_start: 0.7654 (mt0) cc_final: 0.7375 (mt0) REVERT: B 990 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7699 (tp30) outliers start: 50 outliers final: 38 residues processed: 211 average time/residue: 0.3424 time to fit residues: 124.5746 Evaluate side-chains 218 residues out of total 3096 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 1036 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 37 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 423 TYR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 741 TYR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 913 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1067 TYR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain V residue 37 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 0.7980 chunk 299 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 258 optimal weight: 0.7980 chunk 41 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 117 optimal weight: 40.0000 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.197494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150838 restraints weight = 42817.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137659 restraints weight = 57269.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.132973 restraints weight = 42746.986| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29357 Z= 0.256 Angle : 0.658 11.189 39943 Z= 0.310 Chirality : 0.049 0.363 4691 Planarity : 0.004 0.061 5083 Dihedral : 12.053 110.678 5232 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.78 % Allowed : 14.70 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3516 helix: 0.24 (0.21), residues: 622 sheet: -0.30 (0.20), residues: 671 loop : -1.99 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP W 47 HIS 0.005 0.001 HIS A1064 PHE 0.040 0.002 PHE A 238 TYR 0.031 0.001 TYR B1067 ARG 0.005 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.30 seconds wall clock time: 82 minutes 47.43 seconds (4967.43 seconds total)