Starting phenix.real_space_refine on Fri Apr 12 14:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vrw_32108/04_2024/7vrw_32108.pdb" } resolution = 3.6 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16512 2.51 5 N 4260 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 860": "OD1" <-> "OD2" Residue "B ASP 987": "OD1" <-> "OD2" Residue "B GLU 1024": "OE1" <-> "OE2" Residue "B TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 987": "OD1" <-> "OD2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C GLU 1085": "OE1" <-> "OE2" Residue "C PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 25989 Number of models: 1 Model: "" Number of chains: 20 Chain: "B" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8397 Classifications: {'peptide': 1077} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.08, per 1000 atoms: 0.54 Number of scatterers: 25989 At special positions: 0 Unit cell: (149.76, 157.04, 174.72, 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 5103 8.00 N 4260 7.00 C 16512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 731 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B1025 " - pdb=" SG CYS B1036 " distance=2.03 Simple disulfide: pdb=" SG CYS B1075 " - pdb=" SG CYS B1119 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 731 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A1025 " - pdb=" SG CYS A1036 " distance=2.03 Simple disulfide: pdb=" SG CYS A1075 " - pdb=" SG CYS A1119 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 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 538 " - pdb=" SG CYS C 590 " 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 731 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C1025 " - pdb=" SG CYS C1036 " distance=2.03 Simple disulfide: pdb=" SG CYS C1075 " - pdb=" SG CYS C1119 " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 702 " " NAG A1309 " - " ASN A1067 " " NAG A1310 " - " ASN A 165 " " NAG A1311 " - " ASN A 234 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 702 " " NAG B1307 " - " ASN B1067 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 61 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 702 " " NAG C1309 " - " ASN C1067 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN B 710 " " NAG F 1 " - " ASN B 794 " " NAG G 1 " - " ASN B1091 " " NAG H 1 " - " ASN B1127 " " NAG I 1 " - " ASN A 710 " " NAG J 1 " - " ASN A 794 " " NAG K 1 " - " ASN A1091 " " NAG L 1 " - " ASN A1127 " " NAG M 1 " - " ASN C 234 " " NAG N 1 " - " ASN C 710 " " NAG O 1 " - " ASN C 794 " " NAG P 1 " - " ASN C1091 " " NAG Q 1 " - " ASN C1127 " Time building additional restraints: 10.61 Conformation dependent library (CDL) restraints added in 4.5 seconds 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6036 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 57 sheets defined 23.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.805A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.064A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.226A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 418 through 423 removed outlier: 4.086A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 423' Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.649A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.874A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 Processing helix chain 'B' and resid 740 through 750 removed outlier: 3.628A pdb=" N GLY B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 775 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 775 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 Processing helix chain 'B' and resid 842 through 849 Processing helix chain 'B' and resid 859 through 877 Processing helix chain 'B' and resid 879 through 884 removed outlier: 4.120A pdb=" N ALA B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 903 removed outlier: 4.022A pdb=" N ALA B 896 " --> pdb=" O ALA B 892 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR B 897 " --> pdb=" O MET B 893 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 898 " --> pdb=" O GLN B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 912 removed outlier: 4.296A pdb=" N LEU B 909 " --> pdb=" O THR B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 932 Processing helix chain 'B' and resid 934 through 939 removed outlier: 3.911A pdb=" N ALA B 937 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 3.697A pdb=" N ASN B 946 " --> pdb=" O GLN B 942 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN B 948 " --> pdb=" O VAL B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 961 removed outlier: 3.619A pdb=" N SER B 961 " --> pdb=" O GLN B 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 961' Processing helix chain 'B' and resid 978 through 1025 removed outlier: 5.038A pdb=" N VAL B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1140 removed outlier: 3.630A pdb=" N SER B1140 " --> pdb=" O PRO B1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.566A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.206A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.518A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.757A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.862A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 Processing helix chain 'A' and resid 740 through 750 removed outlier: 3.512A pdb=" N GLY A 750 " --> pdb=" O LEU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 775 removed outlier: 3.574A pdb=" N GLN A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 775 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 Processing helix chain 'A' and resid 842 through 849 Processing helix chain 'A' and resid 859 through 878 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.061A pdb=" N ALA A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 removed outlier: 3.824A pdb=" N ALA A 896 " --> pdb=" O ALA A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 912 removed outlier: 4.154A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 932 Processing helix chain 'A' and resid 934 through 939 removed outlier: 3.939A pdb=" N ALA A 937 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 3.816A pdb=" N ASN A 946 " --> pdb=" O GLN A 942 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN A 948 " --> pdb=" O VAL A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 961 removed outlier: 3.559A pdb=" N SER A 961 " --> pdb=" O GLN A 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 961' Processing helix chain 'A' and resid 978 through 1025 removed outlier: 5.141A pdb=" N VAL A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN A 985 " --> pdb=" O GLU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1140 removed outlier: 3.744A pdb=" N SER A1140 " --> pdb=" O PRO A1136 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.764A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 343' Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.200A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 418 through 423 removed outlier: 3.870A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.646A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.871A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 740 through 750 removed outlier: 3.545A pdb=" N GLY C 750 " --> pdb=" O LEU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 751 through 775 removed outlier: 3.559A pdb=" N GLN C 755 " --> pdb=" O SER C 751 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE C 775 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 816 Processing helix chain 'C' and resid 842 through 849 Processing helix chain 'C' and resid 859 through 878 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.138A pdb=" N ALA C 883 " --> pdb=" O TRP C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 902 removed outlier: 3.942A pdb=" N ALA C 896 " --> pdb=" O ALA C 892 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 897 " --> pdb=" O MET C 893 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 912 removed outlier: 4.146A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 932 Processing helix chain 'C' and resid 934 through 939 removed outlier: 3.906A pdb=" N ALA C 937 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 3.769A pdb=" N ASN C 946 " --> pdb=" O GLN C 942 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN C 948 " --> pdb=" O VAL C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 961 removed outlier: 3.571A pdb=" N SER C 961 " --> pdb=" O GLN C 958 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 961' Processing helix chain 'C' and resid 978 through 1025 removed outlier: 4.927A pdb=" N VAL C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1134 through 1140 removed outlier: 3.814A pdb=" N SER C1140 " --> pdb=" O PRO C1136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.608A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.554A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.643A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA6, first strand: chain 'B' and resid 118 through 120 removed outlier: 3.589A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.736A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.801A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.714A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 670 through 675 removed outlier: 3.607A pdb=" N SER B 684 " --> pdb=" O GLN B 675 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 694 through 695 removed outlier: 6.560A pdb=" N ALA B 694 " --> pdb=" O ILE C 781 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 704 through 706 Processing sheet with id=AB6, first strand: chain 'B' and resid 710 through 713 removed outlier: 6.564A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 710 through 713 removed outlier: 6.564A pdb=" N ASN B 710 " --> pdb=" O ALA B1063 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLY B1052 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B1048 " --> pdb=" O GLY B1052 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B1054 " --> pdb=" O PRO B1046 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B1056 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER B1044 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL B1058 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 726 through 729 removed outlier: 4.274A pdb=" N LYS B 726 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 780 through 781 Processing sheet with id=AC1, first strand: chain 'B' and resid 1074 through 1075 Processing sheet with id=AC2, first strand: chain 'B' and resid 1079 through 1083 removed outlier: 4.554A pdb=" N ALA B1080 " --> pdb=" O SER B1116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1116 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1087 through 1089 Processing sheet with id=AC4, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.948A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.522A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AC7, first strand: chain 'A' and resid 101 through 107 removed outlier: 6.244A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 118 through 120 removed outlier: 3.631A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.544A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AD2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.793A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.774A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 670 through 675 removed outlier: 3.591A pdb=" N SER A 684 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 704 through 712 removed outlier: 6.618A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 704 through 712 removed outlier: 6.618A pdb=" N SER A 704 " --> pdb=" O THR A1069 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1069 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA A 706 " --> pdb=" O ASN A1067 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN A1067 " --> pdb=" O ALA A 706 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU A1065 " --> pdb=" O PRO A 708 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A 710 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A1052 " --> pdb=" O ALA A1049 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A1049 " --> pdb=" O GLY A1052 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR A1060 " --> pdb=" O HIS A1041 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS A1041 " --> pdb=" O TYR A1060 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 726 through 729 removed outlier: 4.276A pdb=" N LYS A 726 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 780 through 781 Processing sheet with id=AE1, first strand: chain 'A' and resid 1074 through 1075 Processing sheet with id=AE2, first strand: chain 'A' and resid 1079 through 1083 removed outlier: 4.518A pdb=" N ALA A1080 " --> pdb=" O SER A1116 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A1116 " --> pdb=" O ALA A1080 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1087 through 1089 Processing sheet with id=AE4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.438A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 101 through 107 removed outlier: 6.465A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.715A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.741A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF2, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.028A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF4, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.705A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.481A pdb=" N GLU C 654 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR C 689 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER C 684 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 704 through 706 Processing sheet with id=AF7, first strand: chain 'C' and resid 710 through 712 removed outlier: 6.687A pdb=" N ASN C 710 " --> pdb=" O ALA C1063 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C1058 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 715 through 721 removed outlier: 3.636A pdb=" N GLY C1052 " --> pdb=" O ALA C1049 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C1049 " --> pdb=" O GLY C1052 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 726 through 729 removed outlier: 4.331A pdb=" N LYS C 726 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1074 through 1075 Processing sheet with id=AG2, first strand: chain 'C' and resid 1079 through 1083 removed outlier: 4.511A pdb=" N ALA C1080 " --> pdb=" O SER C1116 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C1116 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1087 through 1090 825 hydrogen bonds defined for protein. 2274 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: 10.78 Time building geometry restraints manager: 11.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8269 1.34 - 1.47: 6825 1.47 - 1.60: 11336 1.60 - 1.73: 0 1.73 - 1.86: 144 Bond restraints: 26574 Sorted by residual: bond pdb=" N VAL B 615 " pdb=" CA VAL B 615 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.14e-02 7.69e+03 1.30e+01 bond pdb=" N VAL B 62 " pdb=" CA VAL B 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.41e+00 bond pdb=" N SER B 60 " pdb=" CA SER B 60 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.48e+00 bond pdb=" N CYS B 617 " pdb=" CA CYS B 617 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.15e-02 7.56e+03 6.31e+00 bond pdb=" N ASN B 616 " pdb=" CA ASN B 616 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.42e-02 4.96e+03 4.83e+00 ... (remaining 26569 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.24: 637 106.24 - 113.18: 14573 113.18 - 120.12: 8868 120.12 - 127.05: 11854 127.05 - 133.99: 236 Bond angle restraints: 36168 Sorted by residual: angle pdb=" N ILE B 418 " pdb=" CA ILE B 418 " pdb=" C ILE B 418 " ideal model delta sigma weight residual 113.20 108.39 4.81 9.60e-01 1.09e+00 2.51e+01 angle pdb=" N ILE C 418 " pdb=" CA ILE C 418 " pdb=" C ILE C 418 " ideal model delta sigma weight residual 113.71 109.72 3.99 9.50e-01 1.11e+00 1.77e+01 angle pdb=" CA CYS C 379 " pdb=" CB CYS C 379 " pdb=" SG CYS C 379 " ideal model delta sigma weight residual 114.40 122.02 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 121.98 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" N GLY C 311 " pdb=" CA GLY C 311 " pdb=" C GLY C 311 " ideal model delta sigma weight residual 111.85 115.31 -3.46 1.06e+00 8.90e-01 1.07e+01 ... (remaining 36163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 15521 23.14 - 46.29: 862 46.29 - 69.43: 120 69.43 - 92.58: 26 92.58 - 115.72: 22 Dihedral angle restraints: 16551 sinusoidal: 7152 harmonic: 9399 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.61 -85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -9.93 -76.07 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -24.88 -61.12 1 1.00e+01 1.00e-02 4.96e+01 ... (remaining 16548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4106 0.103 - 0.206: 141 0.206 - 0.308: 8 0.308 - 0.411: 0 0.411 - 0.514: 2 Chirality restraints: 4257 Sorted by residual: chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 4254 not shown) Planarity restraints: 4663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " -0.125 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" C7 NAG B1309 " 0.036 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " -0.095 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " 0.167 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " -0.087 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO B 139 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " -0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " 0.052 2.00e-02 2.50e+03 4.64e-02 2.69e+01 pdb=" C7 NAG B1308 " -0.006 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.009 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " -0.079 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.041 2.00e-02 2.50e+03 ... (remaining 4660 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 784 2.70 - 3.25: 26089 3.25 - 3.80: 40164 3.80 - 4.35: 51932 4.35 - 4.90: 87040 Nonbonded interactions: 206009 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.154 2.440 nonbonded pdb=" O LYS B 113 " pdb=" OG SER A 469 " model vdw 2.162 2.440 nonbonded pdb=" NE2 GLN B 563 " pdb=" O LYS C 41 " model vdw 2.184 2.520 nonbonded pdb=" OG SER B 469 " pdb=" O LYS C 113 " model vdw 2.189 2.440 nonbonded pdb=" OG1 THR B 385 " pdb=" OG1 THR A 415 " model vdw 2.194 2.440 ... (remaining 206004 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' and (resid 27 through 1140 or resid 1301 through 1309)) 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 8.700 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 69.580 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.320 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 0.055 26574 Z= 0.243 Angle : 0.666 8.604 36168 Z= 0.362 Chirality : 0.046 0.514 4257 Planarity : 0.005 0.132 4620 Dihedral : 14.533 115.724 10398 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.04 % Allowed : 0.18 % Favored : 99.79 % 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: -2.22 (0.14), residues: 3213 helix: 0.52 (0.21), residues: 705 sheet: -1.95 (0.19), residues: 660 loop : -2.17 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 436 HIS 0.010 0.001 HIS B1041 PHE 0.029 0.001 PHE A 562 TYR 0.019 0.001 TYR C 700 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 355 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5499 (mmm) cc_final: 0.5193 (mmm) REVERT: B 177 MET cc_start: 0.3929 (mmm) cc_final: 0.1251 (tmm) REVERT: B 398 ASP cc_start: 0.6907 (m-30) cc_final: 0.6454 (m-30) REVERT: B 733 MET cc_start: 0.7440 (tpp) cc_final: 0.6899 (mmm) REVERT: A 353 TRP cc_start: 0.8045 (p90) cc_final: 0.7734 (p90) REVERT: A 927 ILE cc_start: 0.8411 (tp) cc_final: 0.8208 (tp) REVERT: A 950 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 1128 ASN cc_start: 0.7994 (t0) cc_final: 0.7721 (t0) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.3273 time to fit residues: 194.9448 Evaluate side-chains 236 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 0.0060 chunk 243 optimal weight: 7.9990 chunk 135 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 251 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 0.0270 chunk 187 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A 777 GLN A1094 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26574 Z= 0.150 Angle : 0.564 9.892 36168 Z= 0.282 Chirality : 0.045 0.444 4257 Planarity : 0.004 0.094 4620 Dihedral : 9.045 107.071 4665 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.14 % Allowed : 8.04 % Favored : 90.82 % 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: -1.93 (0.15), residues: 3213 helix: 0.79 (0.20), residues: 711 sheet: -1.72 (0.19), residues: 696 loop : -2.02 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.017 0.001 HIS B 655 PHE 0.024 0.001 PHE C 168 TYR 0.019 0.001 TYR A 265 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 270 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4164 (mmm) cc_final: 0.1362 (tmm) REVERT: B 297 SER cc_start: 0.7823 (m) cc_final: 0.7461 (p) REVERT: B 398 ASP cc_start: 0.7020 (m-30) cc_final: 0.6742 (m-30) REVERT: B 950 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 353 TRP cc_start: 0.8103 (p90) cc_final: 0.7787 (p90) REVERT: A 733 MET cc_start: 0.7385 (mmm) cc_final: 0.7180 (mmm) REVERT: A 927 ILE cc_start: 0.8371 (tp) cc_final: 0.8169 (tp) REVERT: A 950 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7925 (tm-30) REVERT: A 1128 ASN cc_start: 0.7915 (t0) cc_final: 0.7624 (t0) REVERT: C 950 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 1131 TYR cc_start: 0.8188 (t80) cc_final: 0.7968 (t80) outliers start: 32 outliers final: 28 residues processed: 285 average time/residue: 0.3416 time to fit residues: 163.4104 Evaluate side-chains 260 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 464 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 1033 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 242 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 292 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 260 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 580 GLN B 703 ASN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS A1099 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 658 ASN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26574 Z= 0.226 Angle : 0.580 10.825 36168 Z= 0.288 Chirality : 0.045 0.461 4257 Planarity : 0.004 0.071 4620 Dihedral : 8.282 102.009 4665 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.89 % Allowed : 11.49 % Favored : 86.62 % 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: -1.94 (0.14), residues: 3213 helix: 0.74 (0.20), residues: 711 sheet: -1.72 (0.19), residues: 702 loop : -2.01 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.012 0.001 HIS B 655 PHE 0.028 0.001 PHE C 168 TYR 0.011 0.001 TYR B 160 ARG 0.003 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 253 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 398 ASP cc_start: 0.7004 (m-30) cc_final: 0.6803 (m-30) REVERT: B 514 SER cc_start: 0.8472 (m) cc_final: 0.7964 (p) REVERT: B 747 LEU cc_start: 0.8890 (mm) cc_final: 0.8464 (mt) REVERT: B 950 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 1112 ASN cc_start: 0.8286 (m110) cc_final: 0.8060 (m110) REVERT: A 210 ILE cc_start: 0.8075 (pt) cc_final: 0.7872 (pt) REVERT: A 353 TRP cc_start: 0.8270 (p90) cc_final: 0.7896 (p90) REVERT: A 927 ILE cc_start: 0.8478 (tp) cc_final: 0.8265 (tp) REVERT: A 950 GLN cc_start: 0.8497 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 1128 ASN cc_start: 0.7917 (t0) cc_final: 0.7593 (t0) REVERT: C 328 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7082 (mmm-85) REVERT: C 950 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7707 (tm-30) REVERT: C 1131 TYR cc_start: 0.8208 (t80) cc_final: 0.7979 (t80) outliers start: 53 outliers final: 44 residues processed: 279 average time/residue: 0.3185 time to fit residues: 151.0569 Evaluate side-chains 264 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 220 time to evaluate : 2.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 151 optimal weight: 0.0270 chunk 32 optimal weight: 0.0570 chunk 139 optimal weight: 0.0670 chunk 196 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.3294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 207 HIS C 409 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 26574 Z= 0.139 Angle : 0.534 10.225 36168 Z= 0.264 Chirality : 0.044 0.430 4257 Planarity : 0.004 0.055 4620 Dihedral : 7.558 104.797 4665 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.71 % Allowed : 13.63 % Favored : 84.67 % 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: -1.64 (0.15), residues: 3213 helix: 1.03 (0.21), residues: 711 sheet: -1.43 (0.20), residues: 669 loop : -1.89 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.009 0.001 HIS B 655 PHE 0.024 0.001 PHE A 562 TYR 0.018 0.001 TYR B 660 ARG 0.003 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 260 time to evaluate : 2.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4133 (mmm) cc_final: 0.1300 (tmm) REVERT: B 297 SER cc_start: 0.7866 (m) cc_final: 0.7431 (p) REVERT: B 398 ASP cc_start: 0.6992 (m-30) cc_final: 0.6764 (m-30) REVERT: B 514 SER cc_start: 0.8331 (m) cc_final: 0.7902 (p) REVERT: B 602 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7140 (p) REVERT: B 747 LEU cc_start: 0.8892 (mm) cc_final: 0.8510 (mt) REVERT: A 353 TRP cc_start: 0.8202 (p90) cc_final: 0.7951 (p90) REVERT: A 927 ILE cc_start: 0.8376 (tp) cc_final: 0.8157 (tp) REVERT: A 950 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7824 (tm-30) REVERT: A 1128 ASN cc_start: 0.7859 (t0) cc_final: 0.7534 (t0) REVERT: C 328 ARG cc_start: 0.7876 (tpp80) cc_final: 0.6986 (mmm-85) REVERT: C 818 LYS cc_start: 0.7375 (mtmm) cc_final: 0.6985 (ptmt) REVERT: C 950 GLN cc_start: 0.8275 (tm-30) cc_final: 0.7664 (tm-30) REVERT: C 1131 TYR cc_start: 0.8171 (t80) cc_final: 0.7944 (t80) outliers start: 48 outliers final: 34 residues processed: 284 average time/residue: 0.3238 time to fit residues: 156.4764 Evaluate side-chains 266 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 4 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 264 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 278 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 GLN ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN A 865 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 644 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 26574 Z= 0.517 Angle : 0.741 12.321 36168 Z= 0.371 Chirality : 0.050 0.459 4257 Planarity : 0.005 0.064 4620 Dihedral : 7.872 92.061 4665 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.09 % Allowed : 15.01 % Favored : 81.89 % 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: -2.29 (0.14), residues: 3213 helix: 0.12 (0.19), residues: 717 sheet: -1.85 (0.19), residues: 717 loop : -2.12 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 104 HIS 0.010 0.001 HIS A1041 PHE 0.028 0.002 PHE B 392 TYR 0.021 0.002 TYR A 910 ARG 0.009 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 241 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5395 (mmm) cc_final: 0.5135 (mtm) REVERT: B 177 MET cc_start: 0.4185 (mmm) cc_final: 0.1387 (tmm) REVERT: B 398 ASP cc_start: 0.6972 (m-30) cc_final: 0.6636 (m-30) REVERT: B 514 SER cc_start: 0.8781 (m) cc_final: 0.8313 (p) REVERT: B 602 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7449 (p) REVERT: B 660 TYR cc_start: 0.7499 (m-80) cc_final: 0.7195 (m-80) REVERT: B 733 MET cc_start: 0.8273 (mmm) cc_final: 0.7963 (tpp) REVERT: B 950 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 65 PHE cc_start: 0.7629 (m-10) cc_final: 0.7411 (m-10) REVERT: A 104 TRP cc_start: 0.7130 (m-90) cc_final: 0.6655 (m-90) REVERT: A 927 ILE cc_start: 0.8686 (tp) cc_final: 0.8430 (tp) REVERT: A 950 GLN cc_start: 0.8586 (tm-30) cc_final: 0.7950 (tm-30) REVERT: A 1128 ASN cc_start: 0.8122 (t0) cc_final: 0.7780 (t0) REVERT: C 847 LYS cc_start: 0.7841 (tmtt) cc_final: 0.7389 (tttp) REVERT: C 950 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7798 (tm-30) outliers start: 87 outliers final: 67 residues processed: 295 average time/residue: 0.3322 time to fit residues: 166.0732 Evaluate side-chains 278 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 210 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1044 SER Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 865 GLN Chi-restraints excluded: chain C residue 1033 VAL Chi-restraints excluded: chain C residue 1044 SER Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.9980 chunk 279 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 ASN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26574 Z= 0.168 Angle : 0.570 11.324 36168 Z= 0.282 Chirality : 0.045 0.429 4257 Planarity : 0.004 0.062 4620 Dihedral : 7.300 90.759 4665 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.35 % Allowed : 16.93 % Favored : 80.72 % 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: -1.78 (0.15), residues: 3213 helix: 0.73 (0.20), residues: 711 sheet: -1.47 (0.20), residues: 651 loop : -1.91 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS B 655 PHE 0.019 0.001 PHE B 541 TYR 0.013 0.001 TYR B 265 ARG 0.005 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4018 (mmm) cc_final: 0.1271 (tmm) REVERT: B 266 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: B 398 ASP cc_start: 0.7125 (m-30) cc_final: 0.6816 (m-30) REVERT: B 514 SER cc_start: 0.8646 (m) cc_final: 0.8167 (p) REVERT: B 564 GLN cc_start: 0.5266 (OUTLIER) cc_final: 0.4719 (mm-40) REVERT: B 602 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7226 (p) REVERT: B 660 TYR cc_start: 0.7553 (m-80) cc_final: 0.7126 (m-80) REVERT: B 950 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 987 ASP cc_start: 0.6725 (m-30) cc_final: 0.6268 (m-30) REVERT: A 927 ILE cc_start: 0.8486 (tp) cc_final: 0.8221 (tp) REVERT: A 950 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 987 ASP cc_start: 0.6724 (m-30) cc_final: 0.6321 (m-30) REVERT: A 1128 ASN cc_start: 0.8074 (t0) cc_final: 0.7727 (t0) REVERT: C 328 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7194 (mmm-85) REVERT: C 865 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7227 (tp40) REVERT: C 950 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7679 (tm-30) outliers start: 66 outliers final: 46 residues processed: 289 average time/residue: 0.3187 time to fit residues: 157.7566 Evaluate side-chains 272 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 865 GLN Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 175 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 309 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 865 GLN ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26574 Z= 0.255 Angle : 0.594 10.613 36168 Z= 0.293 Chirality : 0.046 0.438 4257 Planarity : 0.004 0.056 4620 Dihedral : 7.141 83.259 4665 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.09 % Allowed : 16.72 % Favored : 80.18 % 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: -1.82 (0.15), residues: 3213 helix: 0.69 (0.20), residues: 711 sheet: -1.52 (0.20), residues: 654 loop : -1.92 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS B 655 PHE 0.018 0.001 PHE A 643 TYR 0.022 0.001 TYR C1103 ARG 0.005 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 230 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4028 (mmm) cc_final: 0.1315 (tmm) REVERT: B 266 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: B 398 ASP cc_start: 0.7148 (m-30) cc_final: 0.6852 (m-30) REVERT: B 514 SER cc_start: 0.8679 (m) cc_final: 0.8244 (p) REVERT: B 546 LEU cc_start: 0.6486 (tt) cc_final: 0.6173 (pp) REVERT: B 564 GLN cc_start: 0.5308 (OUTLIER) cc_final: 0.4779 (mm-40) REVERT: B 602 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7278 (p) REVERT: B 660 TYR cc_start: 0.7607 (m-80) cc_final: 0.7366 (m-80) REVERT: B 733 MET cc_start: 0.8030 (mmm) cc_final: 0.7730 (tpp) REVERT: B 950 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8161 (tm-30) REVERT: B 987 ASP cc_start: 0.6719 (m-30) cc_final: 0.6227 (m-30) REVERT: A 143 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.6160 (t) REVERT: A 153 MET cc_start: 0.4379 (mpp) cc_final: 0.4096 (mpp) REVERT: A 564 GLN cc_start: 0.5320 (OUTLIER) cc_final: 0.4739 (mp-120) REVERT: A 927 ILE cc_start: 0.8535 (tp) cc_final: 0.8258 (tp) REVERT: A 950 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7835 (tm-30) REVERT: A 1128 ASN cc_start: 0.8112 (t0) cc_final: 0.7753 (t0) REVERT: C 847 LYS cc_start: 0.7732 (tmtt) cc_final: 0.7208 (tttp) REVERT: C 950 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 1103 TYR cc_start: 0.8573 (t80) cc_final: 0.8275 (t80) outliers start: 87 outliers final: 68 residues processed: 287 average time/residue: 0.3241 time to fit residues: 159.5857 Evaluate side-chains 295 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 222 time to evaluate : 3.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 210 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 243 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26574 Z= 0.176 Angle : 0.559 10.316 36168 Z= 0.276 Chirality : 0.045 0.431 4257 Planarity : 0.004 0.052 4620 Dihedral : 6.838 76.338 4665 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.74 % Allowed : 17.36 % Favored : 79.90 % 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: -1.64 (0.15), residues: 3213 helix: 0.94 (0.20), residues: 711 sheet: -1.38 (0.20), residues: 657 loop : -1.87 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS B 655 PHE 0.027 0.001 PHE A 562 TYR 0.018 0.001 TYR C1103 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 228 time to evaluate : 2.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4003 (mmm) cc_final: 0.1264 (tmm) REVERT: B 266 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 398 ASP cc_start: 0.7145 (m-30) cc_final: 0.6848 (m-30) REVERT: B 514 SER cc_start: 0.8663 (m) cc_final: 0.8217 (p) REVERT: B 564 GLN cc_start: 0.5294 (OUTLIER) cc_final: 0.4743 (mm-40) REVERT: B 602 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7163 (p) REVERT: B 660 TYR cc_start: 0.7524 (m-80) cc_final: 0.7313 (m-80) REVERT: B 950 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 143 VAL cc_start: 0.6611 (OUTLIER) cc_final: 0.6128 (t) REVERT: A 153 MET cc_start: 0.3977 (mpp) cc_final: 0.3630 (mpp) REVERT: A 177 MET cc_start: 0.4770 (tmm) cc_final: 0.4421 (tmm) REVERT: A 927 ILE cc_start: 0.8448 (tp) cc_final: 0.8184 (tp) REVERT: A 950 GLN cc_start: 0.8534 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 1128 ASN cc_start: 0.7973 (t0) cc_final: 0.7625 (t0) REVERT: C 328 ARG cc_start: 0.7929 (tpp80) cc_final: 0.7216 (mmm-85) REVERT: C 847 LYS cc_start: 0.7779 (tmtt) cc_final: 0.7263 (tttp) REVERT: C 950 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7683 (tm-30) REVERT: C 1103 TYR cc_start: 0.8515 (t80) cc_final: 0.8243 (t80) outliers start: 77 outliers final: 63 residues processed: 278 average time/residue: 0.3254 time to fit residues: 155.9464 Evaluate side-chains 282 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 215 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 995 GLN Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 chunk 288 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 226 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 272 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26574 Z= 0.179 Angle : 0.550 9.657 36168 Z= 0.272 Chirality : 0.045 0.432 4257 Planarity : 0.004 0.049 4620 Dihedral : 6.647 71.760 4665 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.70 % Allowed : 17.47 % Favored : 79.83 % 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: -1.54 (0.15), residues: 3213 helix: 1.06 (0.20), residues: 711 sheet: -1.31 (0.20), residues: 654 loop : -1.81 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS B 655 PHE 0.024 0.001 PHE B 643 TYR 0.017 0.001 TYR A 910 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 237 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.4027 (mmm) cc_final: 0.1281 (tmm) REVERT: B 266 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8088 (m-80) REVERT: B 398 ASP cc_start: 0.7111 (m-30) cc_final: 0.6820 (m-30) REVERT: B 514 SER cc_start: 0.8677 (m) cc_final: 0.8230 (p) REVERT: B 564 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.4808 (mm-40) REVERT: B 602 THR cc_start: 0.7376 (OUTLIER) cc_final: 0.7120 (p) REVERT: B 747 LEU cc_start: 0.8910 (mm) cc_final: 0.8472 (mt) REVERT: A 143 VAL cc_start: 0.6645 (OUTLIER) cc_final: 0.6186 (t) REVERT: A 153 MET cc_start: 0.3578 (mpp) cc_final: 0.3313 (mpp) REVERT: A 177 MET cc_start: 0.4679 (tmm) cc_final: 0.4318 (tmm) REVERT: A 927 ILE cc_start: 0.8439 (tp) cc_final: 0.8181 (tp) REVERT: A 950 GLN cc_start: 0.8515 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 1128 ASN cc_start: 0.7960 (t0) cc_final: 0.7591 (t0) REVERT: C 328 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7216 (mmm-85) REVERT: C 847 LYS cc_start: 0.7803 (tmtt) cc_final: 0.7424 (tttp) REVERT: C 950 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7669 (tm-30) REVERT: C 1103 TYR cc_start: 0.8501 (t80) cc_final: 0.8176 (t80) outliers start: 76 outliers final: 67 residues processed: 283 average time/residue: 0.3272 time to fit residues: 159.0683 Evaluate side-chains 296 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 225 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 1.9990 chunk 304 optimal weight: 0.0070 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 294 optimal weight: 3.9990 chunk 254 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 HIS C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26574 Z= 0.214 Angle : 0.566 10.967 36168 Z= 0.280 Chirality : 0.045 0.428 4257 Planarity : 0.004 0.051 4620 Dihedral : 6.639 68.816 4665 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.63 % Allowed : 17.93 % Favored : 79.44 % 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: -1.52 (0.15), residues: 3213 helix: 1.17 (0.21), residues: 687 sheet: -1.27 (0.20), residues: 669 loop : -1.83 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS B 655 PHE 0.031 0.001 PHE B 643 TYR 0.015 0.001 TYR A 910 ARG 0.003 0.000 ARG C 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6426 Ramachandran restraints generated. 3213 Oldfield, 0 Emsley, 3213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 225 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 MET cc_start: 0.3948 (mmm) cc_final: 0.1227 (tmm) REVERT: B 266 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: B 398 ASP cc_start: 0.7125 (m-30) cc_final: 0.6757 (m-30) REVERT: B 465 GLU cc_start: 0.5743 (pm20) cc_final: 0.5454 (pm20) REVERT: B 514 SER cc_start: 0.8653 (m) cc_final: 0.8216 (p) REVERT: B 602 THR cc_start: 0.7430 (OUTLIER) cc_final: 0.7185 (p) REVERT: B 733 MET cc_start: 0.7974 (mmm) cc_final: 0.7690 (tpp) REVERT: B 747 LEU cc_start: 0.8910 (mm) cc_final: 0.8497 (mt) REVERT: B 950 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 143 VAL cc_start: 0.6650 (OUTLIER) cc_final: 0.6205 (t) REVERT: A 153 MET cc_start: 0.3672 (mpp) cc_final: 0.3390 (mpp) REVERT: A 177 MET cc_start: 0.4714 (tmm) cc_final: 0.4358 (tmm) REVERT: A 927 ILE cc_start: 0.8467 (tp) cc_final: 0.8207 (tp) REVERT: A 950 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7796 (tm-30) REVERT: A 1128 ASN cc_start: 0.8058 (t0) cc_final: 0.7693 (t0) REVERT: C 328 ARG cc_start: 0.7945 (tpp80) cc_final: 0.7204 (mmm-85) REVERT: C 847 LYS cc_start: 0.7833 (tmtt) cc_final: 0.7467 (tttp) REVERT: C 950 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 1103 TYR cc_start: 0.8506 (t80) cc_final: 0.8178 (t80) outliers start: 74 outliers final: 68 residues processed: 272 average time/residue: 0.3227 time to fit residues: 151.5706 Evaluate side-chains 288 residues out of total 2814 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 217 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 724 MET Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain B residue 1077 ASP Chi-restraints excluded: chain B residue 1097 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 660 TYR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 731 CYS Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1097 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 349 SER Chi-restraints excluded: chain C residue 388 ASN Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 MET Chi-restraints excluded: chain C residue 768 ASP Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 1097 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.9980 chunk 271 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 255 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.168905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138058 restraints weight = 40331.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137858 restraints weight = 50431.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.139385 restraints weight = 50968.282| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26574 Z= 0.276 Angle : 0.600 10.578 36168 Z= 0.298 Chirality : 0.046 0.427 4257 Planarity : 0.004 0.054 4620 Dihedral : 6.753 65.280 4665 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.88 % Allowed : 17.72 % Favored : 79.40 % 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: -1.64 (0.15), residues: 3213 helix: 1.01 (0.20), residues: 687 sheet: -1.33 (0.20), residues: 669 loop : -1.89 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS B 655 PHE 0.032 0.002 PHE B 643 TYR 0.018 0.001 TYR A 910 ARG 0.003 0.000 ARG B 898 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.53 seconds wall clock time: 83 minutes 48.76 seconds (5028.76 seconds total)