Starting phenix.real_space_refine on Sun Nov 19 11:48:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xns_33325/11_2023/7xns_33325.pdb" } resolution = 3.48 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= 0.060 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16941 2.51 5 N 4341 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 40": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1092": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 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 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 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 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 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 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 chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 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 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 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 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 chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 13.49, per 1000 atoms: 0.51 Number of scatterers: 26595 At special positions: 0 Unit cell: (154.08, 153.01, 181.9, 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 114 16.00 O 5199 8.00 N 4341 7.00 C 16941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " 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 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=0, 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 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 331 " " NAG C1310 " - " ASN C 343 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 616 " " NAG K 1 " - " ASN B 709 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 616 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 10.71 Conformation dependent library (CDL) restraints added in 4.6 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 45 sheets defined 23.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.911A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.573A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.582A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.621A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.999A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.612A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.175A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.617A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.247A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.720A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.081A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.335A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 4.169A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.908A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.686A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.583A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.661A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.568A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 removed outlier: 3.728A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.125A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.816A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.286A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.607A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.703A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.149A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.218A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 4.160A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.903A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.528A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.595A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.579A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.947A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.728A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.230A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.642A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.290A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.630A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.730A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.121A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.352A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1150 removed outlier: 4.030A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C1149 " --> pdb=" O LEU C1145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1150 " --> pdb=" O ASP C1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.879A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.511A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.809A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.748A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.627A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.257A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.839A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 568 removed outlier: 3.964A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.650A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.111A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.910A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.512A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.901A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.826A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.573A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.282A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.826A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 567 through 568 removed outlier: 3.965A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.617A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.055A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.896A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.970A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.860A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.338A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.803A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.628A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.244A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.836A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 567 through 568 removed outlier: 3.951A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.111A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 833 hydrogen bonds defined for protein. 2298 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: 12.20 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8418 1.34 - 1.46: 6742 1.46 - 1.58: 11921 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 27225 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 27220 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 792 106.58 - 113.43: 15020 113.43 - 120.28: 9436 120.28 - 127.13: 11572 127.13 - 133.98: 257 Bond angle restraints: 37077 Sorted by residual: angle pdb=" C THR A 333 " pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C THR C 333 " pdb=" N ASN C 334 " pdb=" CA ASN C 334 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ASP B1041 " pdb=" CA ASP B1041 " pdb=" CB ASP B1041 " ideal model delta sigma weight residual 113.15 108.25 4.90 1.63e+00 3.76e-01 9.05e+00 angle pdb=" CA ASP B1041 " pdb=" CB ASP B1041 " pdb=" CG ASP B1041 " ideal model delta sigma weight residual 112.60 115.58 -2.98 1.00e+00 1.00e+00 8.89e+00 ... (remaining 37072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 14188 17.73 - 35.45: 1178 35.45 - 53.18: 211 53.18 - 70.91: 40 70.91 - 88.63: 28 Dihedral angle restraints: 15645 sinusoidal: 6078 harmonic: 9567 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.73 68.73 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.64 68.64 1 1.00e+01 1.00e-02 6.10e+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 -154.26 68.26 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 15642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3901 0.082 - 0.164: 443 0.164 - 0.246: 15 0.246 - 0.328: 0 0.328 - 0.410: 6 Chirality restraints: 4365 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 4362 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1041 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ASP A1041 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A1041 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A1042 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO C 230 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 230 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.029 5.00e-02 4.00e+02 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5858 2.78 - 3.31: 24187 3.31 - 3.84: 40275 3.84 - 4.37: 45339 4.37 - 4.90: 79900 Nonbonded interactions: 195559 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.252 2.440 nonbonded pdb=" NE2 HIS B 66 " pdb=" OG1 THR B 250 " model vdw 2.285 2.520 nonbonded pdb=" NZ LYS A 825 " pdb=" O LEU A 938 " model vdw 2.287 2.520 nonbonded pdb=" NZ LYS B 825 " pdb=" O LEU B 938 " model vdw 2.290 2.520 nonbonded pdb=" NE2 HIS A 66 " pdb=" OG1 THR A 250 " model vdw 2.291 2.520 ... (remaining 195554 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' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.460 Check model and map are aligned: 0.390 Set scattering table: 0.230 Process input model: 72.200 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.004 0.044 27225 Z= 0.287 Angle : 0.652 7.471 37077 Z= 0.339 Chirality : 0.049 0.410 4365 Planarity : 0.004 0.055 4722 Dihedral : 13.572 88.634 9393 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3267 helix: 1.59 (0.22), residues: 687 sheet: -0.14 (0.20), residues: 666 loop : -1.35 (0.14), residues: 1914 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3793 time to fit residues: 208.6643 Evaluate side-chains 202 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 2.886 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.7980 chunk 247 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 132 optimal weight: 0.0030 chunk 256 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A1119 ASN B 148 ASN B 207 HIS C 148 ASN C 564 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27225 Z= 0.168 Angle : 0.573 13.396 37077 Z= 0.287 Chirality : 0.046 0.333 4365 Planarity : 0.004 0.049 4722 Dihedral : 4.377 27.358 3528 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.95 % Allowed : 6.86 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.15), residues: 3267 helix: 1.62 (0.22), residues: 693 sheet: -0.22 (0.20), residues: 669 loop : -1.39 (0.13), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 3.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 240 average time/residue: 0.3443 time to fit residues: 139.4055 Evaluate side-chains 201 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 186 time to evaluate : 2.977 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2351 time to fit residues: 10.7353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 202 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 264 optimal weight: 40.0000 chunk 295 optimal weight: 0.1980 chunk 101 optimal weight: 0.8980 chunk 238 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN A 613 GLN C 658 ASN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27225 Z= 0.178 Angle : 0.550 10.100 37077 Z= 0.273 Chirality : 0.045 0.333 4365 Planarity : 0.004 0.050 4722 Dihedral : 4.241 22.456 3528 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.30 % Allowed : 9.98 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.15), residues: 3267 helix: 1.85 (0.22), residues: 669 sheet: -0.08 (0.20), residues: 642 loop : -1.39 (0.13), residues: 1956 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 209 time to evaluate : 2.774 Fit side-chains outliers start: 37 outliers final: 23 residues processed: 234 average time/residue: 0.3679 time to fit residues: 143.3991 Evaluate side-chains 209 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2335 time to fit residues: 14.1319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 141 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 chunk 316 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 282 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 564 GLN A 658 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 148 ASN B 196 ASN B 506 GLN B 564 GLN B 613 GLN B 658 ASN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 613 GLN C 658 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 27225 Z= 0.546 Angle : 0.762 15.050 37077 Z= 0.390 Chirality : 0.053 0.343 4365 Planarity : 0.005 0.058 4722 Dihedral : 5.063 25.494 3528 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.17 % Allowed : 13.10 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.14), residues: 3267 helix: 1.06 (0.21), residues: 666 sheet: -0.56 (0.20), residues: 669 loop : -1.68 (0.13), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 210 time to evaluate : 2.930 Fit side-chains outliers start: 62 outliers final: 36 residues processed: 253 average time/residue: 0.3462 time to fit residues: 147.8615 Evaluate side-chains 223 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 187 time to evaluate : 3.084 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.2371 time to fit residues: 20.3989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 0.0980 chunk 179 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN B 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 27225 Z= 0.177 Angle : 0.576 10.946 37077 Z= 0.290 Chirality : 0.046 0.324 4365 Planarity : 0.004 0.054 4722 Dihedral : 4.539 25.088 3528 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.09 % Allowed : 14.29 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3267 helix: 1.63 (0.22), residues: 669 sheet: -0.37 (0.20), residues: 657 loop : -1.56 (0.13), residues: 1941 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 3.063 Fit side-chains outliers start: 31 outliers final: 15 residues processed: 231 average time/residue: 0.3506 time to fit residues: 136.9597 Evaluate side-chains 203 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 2.931 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.2500 time to fit residues: 11.0883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 2.9990 chunk 284 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 27225 Z= 0.333 Angle : 0.625 9.402 37077 Z= 0.317 Chirality : 0.047 0.331 4365 Planarity : 0.005 0.056 4722 Dihedral : 4.599 25.353 3528 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.65 % Allowed : 15.72 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3267 helix: 1.77 (0.22), residues: 651 sheet: -0.67 (0.19), residues: 705 loop : -1.59 (0.13), residues: 1911 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 185 time to evaluate : 2.828 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 27 residues processed: 220 average time/residue: 0.3451 time to fit residues: 128.5826 Evaluate side-chains 207 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.824 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.2435 time to fit residues: 16.4938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 180 optimal weight: 0.7980 chunk 231 optimal weight: 0.5980 chunk 179 optimal weight: 1.9990 chunk 266 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 192 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN B 658 ASN C 872 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27225 Z= 0.176 Angle : 0.559 9.792 37077 Z= 0.279 Chirality : 0.045 0.324 4365 Planarity : 0.004 0.054 4722 Dihedral : 4.354 23.998 3528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.91 % Allowed : 15.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3267 helix: 2.06 (0.22), residues: 651 sheet: -0.57 (0.19), residues: 711 loop : -1.51 (0.13), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 2.846 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 218 average time/residue: 0.3397 time to fit residues: 125.2081 Evaluate side-chains 201 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 187 time to evaluate : 2.965 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.2598 time to fit residues: 10.7645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 247 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN B 658 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27225 Z= 0.223 Angle : 0.576 10.233 37077 Z= 0.287 Chirality : 0.046 0.324 4365 Planarity : 0.004 0.055 4722 Dihedral : 4.324 23.551 3528 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.05 % Allowed : 16.42 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3267 helix: 2.01 (0.22), residues: 654 sheet: -0.55 (0.19), residues: 711 loop : -1.50 (0.13), residues: 1902 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 194 time to evaluate : 3.092 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 216 average time/residue: 0.3463 time to fit residues: 126.5189 Evaluate side-chains 205 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 2.805 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2386 time to fit residues: 12.5238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 293 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 265 optimal weight: 30.0000 chunk 277 optimal weight: 7.9990 chunk 292 optimal weight: 0.7980 chunk 192 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN B 658 ASN B 957 GLN C 957 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27225 Z= 0.223 Angle : 0.576 10.586 37077 Z= 0.288 Chirality : 0.046 0.324 4365 Planarity : 0.004 0.055 4722 Dihedral : 4.303 23.138 3528 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.53 % Allowed : 16.67 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3267 helix: 2.05 (0.22), residues: 654 sheet: -0.53 (0.20), residues: 708 loop : -1.48 (0.13), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 3.161 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 200 average time/residue: 0.3631 time to fit residues: 122.6731 Evaluate side-chains 188 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 180 time to evaluate : 3.102 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2372 time to fit residues: 7.6514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 325 optimal weight: 3.9990 chunk 299 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27225 Z= 0.177 Angle : 0.566 11.976 37077 Z= 0.280 Chirality : 0.045 0.322 4365 Planarity : 0.004 0.055 4722 Dihedral : 4.174 22.123 3528 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.28 % Allowed : 16.91 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3267 helix: 2.18 (0.22), residues: 654 sheet: -0.48 (0.20), residues: 711 loop : -1.43 (0.13), residues: 1902 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 2.859 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 195 average time/residue: 0.3707 time to fit residues: 121.5627 Evaluate side-chains 184 residues out of total 2871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 2.890 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2806 time to fit residues: 6.6533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 259 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 266 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 957 GLN ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.174665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122594 restraints weight = 40300.380| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.78 r_work: 0.3377 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27225 Z= 0.369 Angle : 0.639 11.317 37077 Z= 0.322 Chirality : 0.048 0.328 4365 Planarity : 0.005 0.057 4722 Dihedral : 4.474 22.259 3528 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.49 % Allowed : 16.98 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3267 helix: 1.84 (0.22), residues: 654 sheet: -0.64 (0.20), residues: 705 loop : -1.57 (0.13), residues: 1908 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5112.57 seconds wall clock time: 94 minutes 51.03 seconds (5691.03 seconds total)