Starting phenix.real_space_refine on Fri Aug 9 06:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h10_34420/08_2024/8h10_34420.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 135 5.16 5 C 15894 2.51 5 N 4035 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ASP 57": "OD1" <-> "OD2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A ASP 557": "OD1" <-> "OD2" Residue "A TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 57": "OD1" <-> "OD2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 183": "NH1" <-> "NH2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 296": "OD1" <-> "OD2" Residue "B TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 502": "OE1" <-> "OE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 502": "OE1" <-> "OE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24882 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "B" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 Chain: "C" Number of atoms: 8007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8007 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 51, 'TRANS': 974} Chain breaks: 6 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: "A" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 259 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 14} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 14.13, per 1000 atoms: 0.57 Number of scatterers: 24882 At special positions: 0 Unit cell: (122.64, 127.02, 177.39, 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 135 16.00 O 4818 8.00 N 4035 7.00 C 15894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.04 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.04 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.03 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.04 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.04 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.04 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.04 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.03 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.01 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.04 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.02 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.04 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.03 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.01 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.04 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-ASN " NAG A1301 " - " ASN A 65 " " NAG A1302 " - " ASN A1080 " " NAG A1303 " - " ASN A 109 " " NAG A1304 " - " ASN A 119 " " NAG A1305 " - " ASN A 158 " " NAG A1306 " - " ASN A 269 " " NAG A1307 " - " ASN A 318 " " NAG A1308 " - " ASN A 357 " " NAG A1309 " - " ASN A 602 " " NAG A1310 " - " ASN A 691 " " NAG A1311 " - " ASN A 699 " " NAG A1312 " - " ASN A 783 " " NAG A1313 " - " ASN A1056 " " NAG A1315 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1302 " - " ASN B1080 " " NAG B1303 " - " ASN B 109 " " NAG B1304 " - " ASN B 119 " " NAG B1305 " - " ASN B 158 " " NAG B1306 " - " ASN B 269 " " NAG B1307 " - " ASN B 318 " " NAG B1308 " - " ASN B 357 " " NAG B1309 " - " ASN B 602 " " NAG B1310 " - " ASN B 691 " " NAG B1311 " - " ASN B 699 " " NAG B1312 " - " ASN B 783 " " NAG B1313 " - " ASN B1056 " " NAG B1315 " - " ASN B1116 " " NAG C1302 " - " ASN C 65 " " NAG C1303 " - " ASN C1080 " " NAG C1304 " - " ASN C 109 " " NAG C1305 " - " ASN C 119 " " NAG C1306 " - " ASN C 158 " " NAG C1307 " - " ASN C 269 " " NAG C1308 " - " ASN C 318 " " NAG C1309 " - " ASN C 357 " " NAG C1310 " - " ASN C 602 " " NAG C1311 " - " ASN C 691 " " NAG C1312 " - " ASN C 699 " " NAG C1313 " - " ASN C 783 " " NAG C1314 " - " ASN C1056 " " NAG C1316 " - " ASN C1116 " " NAG D 1 " - " ASN A 227 " " NAG E 1 " - " ASN B 227 " " NAG F 1 " - " ASN C 227 " Time building additional restraints: 9.48 Conformation dependent library (CDL) restraints added in 4.3 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 48 sheets defined 26.8% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR A 356 " --> pdb=" O SER A 353 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN A 357 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 357' Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.656A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 3.515A pdb=" N ASP A 393 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.706A pdb=" N ASP A 429 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 430' Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.542A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 492 " --> pdb=" O ILE A 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 602 through 604 No H-bonds generated for 'chain 'A' and resid 602 through 604' Processing helix chain 'A' and resid 605 through 611 removed outlier: 3.611A pdb=" N ALA A 609 " --> pdb=" O ASP A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 615 removed outlier: 3.505A pdb=" N LEU A 615 " --> pdb=" O ALA A 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 612 through 615' Processing helix chain 'A' and resid 616 through 621 removed outlier: 3.620A pdb=" N ILE A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 728 through 737 removed outlier: 3.934A pdb=" N GLN A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 765 removed outlier: 3.744A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG A 747 " --> pdb=" O THR A 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 748 " --> pdb=" O GLN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 788 removed outlier: 3.799A pdb=" N LEU A 788 " --> pdb=" O SER A 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 785 through 788' Processing helix chain 'A' and resid 798 through 805 Processing helix chain 'A' and resid 831 through 838 Processing helix chain 'A' and resid 848 through 866 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU A 898 " --> pdb=" O THR A 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 963 removed outlier: 3.743A pdb=" N ILE A 962 " --> pdb=" O VAL A 958 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 958 through 963' Processing helix chain 'A' and resid 967 through 1015 removed outlier: 3.739A pdb=" N VAL A 973 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASN B 357 " --> pdb=" O VAL B 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 357' Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.657A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 3.514A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.706A pdb=" N ASP B 429 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 425 through 430' Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.543A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 492 " --> pdb=" O ILE B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 492' Processing helix chain 'B' and resid 602 through 604 No H-bonds generated for 'chain 'B' and resid 602 through 604' Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.612A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 615 removed outlier: 3.506A pdb=" N LEU B 615 " --> pdb=" O ALA B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 615' Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.621A pdb=" N ILE B 621 " --> pdb=" O PRO B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 728 through 737 removed outlier: 3.934A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 765 removed outlier: 3.742A pdb=" N ASN B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG B 747 " --> pdb=" O THR B 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 748 " --> pdb=" O GLN B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 788 removed outlier: 3.799A pdb=" N LEU B 788 " --> pdb=" O SER B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 798 through 805 Processing helix chain 'B' and resid 831 through 838 Processing helix chain 'B' and resid 848 through 866 Processing helix chain 'B' and resid 879 through 890 Processing helix chain 'B' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 922 Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 963 removed outlier: 3.743A pdb=" N ILE B 962 " --> pdb=" O VAL B 958 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 958 through 963' Processing helix chain 'B' and resid 967 through 1015 removed outlier: 3.738A pdb=" N VAL B 973 " --> pdb=" O VAL B 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 324 through 330 Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.568A pdb=" N TYR C 356 " --> pdb=" O SER C 353 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN C 357 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 353 through 357' Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.657A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 3.514A pdb=" N ASP C 393 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 394 " --> pdb=" O GLY C 391 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.707A pdb=" N ASP C 429 " --> pdb=" O THR C 425 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 430' Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.543A pdb=" N TYR C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN C 492 " --> pdb=" O ILE C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 492' Processing helix chain 'C' and resid 602 through 604 No H-bonds generated for 'chain 'C' and resid 602 through 604' Processing helix chain 'C' and resid 605 through 611 removed outlier: 3.612A pdb=" N ALA C 609 " --> pdb=" O ASP C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 615 removed outlier: 3.505A pdb=" N LEU C 615 " --> pdb=" O ALA C 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 612 through 615' Processing helix chain 'C' and resid 616 through 621 removed outlier: 3.620A pdb=" N ILE C 621 " --> pdb=" O PRO C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 Processing helix chain 'C' and resid 728 through 737 removed outlier: 3.935A pdb=" N GLN C 737 " --> pdb=" O ASN C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 765 removed outlier: 3.742A pdb=" N ASN C 746 " --> pdb=" O CYS C 742 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG C 747 " --> pdb=" O THR C 743 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 748 " --> pdb=" O GLN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 788 removed outlier: 3.800A pdb=" N LEU C 788 " --> pdb=" O SER C 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 785 through 788' Processing helix chain 'C' and resid 798 through 805 Processing helix chain 'C' and resid 831 through 838 Processing helix chain 'C' and resid 848 through 866 Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 894 through 901 removed outlier: 4.347A pdb=" N LEU C 898 " --> pdb=" O THR C 894 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 922 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.573A pdb=" N GLN C 931 " --> pdb=" O LEU C 927 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 963 removed outlier: 3.743A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 958 through 963' Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.738A pdb=" N VAL C 973 " --> pdb=" O VAL C 969 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN A 230 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 103 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 232 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP A 101 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE A 234 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASN A 118 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 161 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.516A pdb=" N PHE A 529 " --> pdb=" O LEU A 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL A 382 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 502 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.643A pdb=" N CYS A 348 " --> pdb=" O CYS A 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA9, first strand: chain 'A' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.063A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.718A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A1032 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.519A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 769 through 771 Processing sheet with id=AB7, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB8, first strand: chain 'A' and resid 1102 through 1104 Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU B 194 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS B 221 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL B 196 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR B 200 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N THR B 215 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N VAL B 40 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN B 230 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE B 103 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG B 232 " --> pdb=" O TRP B 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP B 101 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE B 234 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN B 118 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 315 removed outlier: 3.517A pdb=" N PHE B 529 " --> pdb=" O LEU B 532 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.954A pdb=" N VAL B 382 " --> pdb=" O ILE B 345 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU B 502 " --> pdb=" O ASN B 381 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.642A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AC8, first strand: chain 'B' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.064A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.829A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.685A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET B1032 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR B1049 " --> pdb=" O HIS B1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS B1030 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.685A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 718 removed outlier: 4.521A pdb=" N LYS B 715 " --> pdb=" O LEU B 843 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD6, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id=AD7, first strand: chain 'C' and resid 32 through 34 removed outlier: 7.789A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 51 through 59 removed outlier: 3.941A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 81 through 82 removed outlier: 7.073A pdb=" N ASN C 230 " --> pdb=" O PHE C 103 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE C 103 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 232 " --> pdb=" O TRP C 101 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TRP C 101 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE C 234 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ASN C 118 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE C 161 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AE2, first strand: chain 'C' and resid 312 through 315 removed outlier: 3.517A pdb=" N PHE C 529 " --> pdb=" O LEU C 532 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.955A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU C 502 " --> pdb=" O ASN C 381 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.643A pdb=" N CYS C 348 " --> pdb=" O CYS C 511 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE6, first strand: chain 'C' and resid 537 through 540 removed outlier: 5.211A pdb=" N ASP C 560 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER C 561 " --> pdb=" O GLY C 552 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.063A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.684A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 715 through 718 removed outlier: 4.520A pdb=" N LYS C 715 " --> pdb=" O LEU C 843 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF3, first strand: chain 'C' and resid 1102 through 1104 968 hydrogen bonds defined for protein. 2661 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.62 Time building geometry restraints manager: 10.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4011 1.31 - 1.44: 7158 1.44 - 1.58: 14097 1.58 - 1.71: 0 1.71 - 1.84: 180 Bond restraints: 25446 Sorted by residual: bond pdb=" C1C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C1C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.368 1.534 -0.166 2.00e-02 2.50e+03 6.85e+01 bond pdb=" C1C BLA A1314 " pdb=" NC BLA A1314 " ideal model delta sigma weight residual 1.368 1.533 -0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C4C BLA B1314 " pdb=" NC BLA B1314 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" C4C BLA C1315 " pdb=" NC BLA C1315 " ideal model delta sigma weight residual 1.375 1.538 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 25441 not shown) Histogram of bond angle deviations from ideal: 98.91 - 105.94: 581 105.94 - 112.96: 13570 112.96 - 119.99: 8491 119.99 - 127.02: 11741 127.02 - 134.04: 228 Bond angle restraints: 34611 Sorted by residual: angle pdb=" N ASN A 589 " pdb=" CA ASN A 589 " pdb=" C ASN A 589 " ideal model delta sigma weight residual 114.64 106.26 8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" N ASN C 589 " pdb=" CA ASN C 589 " pdb=" C ASN C 589 " ideal model delta sigma weight residual 114.64 106.27 8.37 1.52e+00 4.33e-01 3.03e+01 angle pdb=" N ASN B 589 " pdb=" CA ASN B 589 " pdb=" C ASN B 589 " ideal model delta sigma weight residual 114.64 106.31 8.33 1.52e+00 4.33e-01 3.00e+01 angle pdb=" CA GLN C1124 " pdb=" CB GLN C1124 " pdb=" CG GLN C1124 " ideal model delta sigma weight residual 114.10 123.72 -9.62 2.00e+00 2.50e-01 2.31e+01 angle pdb=" CA GLN A1124 " pdb=" CB GLN A1124 " pdb=" CG GLN A1124 " ideal model delta sigma weight residual 114.10 123.69 -9.59 2.00e+00 2.50e-01 2.30e+01 ... (remaining 34606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 14072 15.24 - 30.47: 1258 30.47 - 45.71: 324 45.71 - 60.94: 99 60.94 - 76.18: 36 Dihedral angle restraints: 15789 sinusoidal: 6813 harmonic: 8976 Sorted by residual: dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.63 68.63 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS A 467 " pdb=" SG CYS A 467 " pdb=" SG CYS A 474 " pdb=" CB CYS A 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.61 68.61 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS C 467 " pdb=" SG CYS C 467 " pdb=" SG CYS C 474 " pdb=" CB CYS C 474 " ideal model delta sinusoidal sigma weight residual -86.00 -154.60 68.60 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 15786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3436 0.077 - 0.153: 549 0.153 - 0.230: 44 0.230 - 0.306: 0 0.306 - 0.383: 3 Chirality restraints: 4032 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 3.77e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 65 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 65 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4029 not shown) Planarity restraints: 4449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA C1315 " -0.221 2.00e-02 2.50e+03 2.63e-01 1.72e+03 pdb=" C1A BLA C1315 " 0.613 2.00e-02 2.50e+03 pdb=" C1D BLA C1315 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA C1315 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA C1315 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA C1315 " -0.244 2.00e-02 2.50e+03 pdb=" CAD BLA C1315 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA C1315 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA C1315 " 0.036 2.00e-02 2.50e+03 pdb=" CMD BLA C1315 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA B1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA B1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA B1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA B1314 " 0.057 2.00e-02 2.50e+03 pdb=" C3D BLA B1314 " -0.060 2.00e-02 2.50e+03 pdb=" C4D BLA B1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA B1314 " -0.010 2.00e-02 2.50e+03 pdb=" CHA BLA B1314 " -0.370 2.00e-02 2.50e+03 pdb=" CHD BLA B1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA B1314 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1314 " -0.221 2.00e-02 2.50e+03 2.62e-01 1.72e+03 pdb=" C1A BLA A1314 " 0.612 2.00e-02 2.50e+03 pdb=" C1D BLA A1314 " -0.045 2.00e-02 2.50e+03 pdb=" C2D BLA A1314 " 0.058 2.00e-02 2.50e+03 pdb=" C3D BLA A1314 " -0.061 2.00e-02 2.50e+03 pdb=" C4D BLA A1314 " -0.243 2.00e-02 2.50e+03 pdb=" CAD BLA A1314 " -0.011 2.00e-02 2.50e+03 pdb=" CHA BLA A1314 " -0.369 2.00e-02 2.50e+03 pdb=" CHD BLA A1314 " 0.037 2.00e-02 2.50e+03 pdb=" CMD BLA A1314 " 0.243 2.00e-02 2.50e+03 ... (remaining 4446 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7537 2.82 - 3.34: 20022 3.34 - 3.86: 38480 3.86 - 4.38: 44658 4.38 - 4.90: 79807 Nonbonded interactions: 190504 Sorted by model distance: nonbonded pdb=" OH TYR C 436 " pdb=" OH TYR C 484 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.305 3.040 nonbonded pdb=" OH TYR B 436 " pdb=" OH TYR B 484 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG A1073 " pdb=" O ASP A1100 " model vdw 2.325 3.120 nonbonded pdb=" NH1 ARG B1073 " pdb=" O ASP B1100 " model vdw 2.326 3.120 ... (remaining 190499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 31 through 1125 or resid 1302 through 1313)) selection = (chain 'B' and (resid 31 through 1125 or resid 1302 through 1313)) selection = (chain 'C' and (resid 31 through 1125 or resid 1302 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 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: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 68.430 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:10.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.008 0.166 25446 Z= 0.512 Angle : 0.901 11.693 34611 Z= 0.475 Chirality : 0.055 0.383 4032 Planarity : 0.010 0.263 4404 Dihedral : 12.960 76.178 9894 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.64 % Allowed : 1.05 % Favored : 98.31 % 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: -1.07 (0.14), residues: 3036 helix: -0.06 (0.20), residues: 684 sheet: 0.91 (0.20), residues: 717 loop : -1.84 (0.13), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 868 HIS 0.005 0.001 HIS B1040 PHE 0.038 0.002 PHE A 888 TYR 0.039 0.002 TYR C1120 ARG 0.006 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 2.647 Fit side-chains revert: symmetry clash REVERT: C 543 LYS cc_start: 0.7849 (tttm) cc_final: 0.7595 (mttt) REVERT: C 679 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7485 (ptp) REVERT: C 1032 MET cc_start: 0.8791 (ptm) cc_final: 0.8464 (ptp) outliers start: 17 outliers final: 0 residues processed: 279 average time/residue: 1.2744 time to fit residues: 412.8640 Evaluate side-chains 162 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 679 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 0.0010 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 145 optimal weight: 0.0770 chunk 178 optimal weight: 1.9990 chunk 277 optimal weight: 0.8980 overall best weight: 0.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN A 632 GLN A 883 GLN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 GLN B 632 GLN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 523 GLN C 632 GLN C 883 GLN ** C 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25446 Z= 0.146 Angle : 0.549 7.575 34611 Z= 0.284 Chirality : 0.044 0.333 4032 Planarity : 0.005 0.108 4404 Dihedral : 7.792 85.490 4437 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 8.39 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 3036 helix: 1.03 (0.21), residues: 669 sheet: 0.81 (0.19), residues: 753 loop : -1.61 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 868 HIS 0.003 0.001 HIS B1046 PHE 0.014 0.001 PHE C 548 TYR 0.019 0.001 TYR A 352 ARG 0.007 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 2.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 882 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8327 (mtp) REVERT: C 56 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6775 (pt0) outliers start: 29 outliers final: 9 residues processed: 176 average time/residue: 1.0598 time to fit residues: 225.7934 Evaluate side-chains 156 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 145 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 882 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 946 LYS Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 967 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 278 optimal weight: 0.0020 chunk 300 optimal weight: 0.0000 chunk 247 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 ASN A 889 ASN B 733 ASN B 746 ASN B 889 ASN C 733 ASN C 746 ASN C 889 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.004 0.041 25446 Z= 0.286 Angle : 0.585 7.542 34611 Z= 0.306 Chirality : 0.046 0.340 4032 Planarity : 0.005 0.105 4404 Dihedral : 7.293 89.264 4434 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.91 % Allowed : 10.26 % Favored : 87.83 % 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: -0.48 (0.15), residues: 3036 helix: 1.17 (0.21), residues: 684 sheet: 0.75 (0.19), residues: 747 loop : -1.58 (0.14), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 868 HIS 0.006 0.001 HIS A1046 PHE 0.027 0.002 PHE A 888 TYR 0.023 0.002 TYR A 352 ARG 0.007 0.001 ARG C1073 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: A 333 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7840 (pptt) REVERT: C 181 HIS cc_start: 0.6035 (OUTLIER) cc_final: 0.5604 (p90) REVERT: C 850 ASP cc_start: 0.7549 (m-30) cc_final: 0.7340 (m-30) outliers start: 51 outliers final: 25 residues processed: 187 average time/residue: 1.0047 time to fit residues: 229.4624 Evaluate side-chains 170 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 GLN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 733 ASN Chi-restraints excluded: chain B residue 768 LYS Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 181 HIS Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 733 ASN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25446 Z= 0.235 Angle : 0.546 6.938 34611 Z= 0.286 Chirality : 0.045 0.327 4032 Planarity : 0.005 0.102 4404 Dihedral : 6.914 89.372 4434 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.72 % Allowed : 12.25 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 3036 helix: 1.43 (0.22), residues: 666 sheet: 0.77 (0.19), residues: 747 loop : -1.48 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 868 HIS 0.006 0.001 HIS B1046 PHE 0.018 0.001 PHE B 888 TYR 0.021 0.001 TYR B 352 ARG 0.003 0.000 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 155 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7399 (mt) REVERT: A 333 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7742 (pttp) REVERT: C 151 MET cc_start: 0.3589 (OUTLIER) cc_final: 0.2800 (ptp) outliers start: 46 outliers final: 23 residues processed: 192 average time/residue: 0.9938 time to fit residues: 233.2234 Evaluate side-chains 170 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 967 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 220 optimal weight: 0.0670 chunk 122 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN A 883 GLN B 546 GLN B 733 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25446 Z= 0.385 Angle : 0.631 7.787 34611 Z= 0.331 Chirality : 0.048 0.335 4032 Planarity : 0.005 0.093 4404 Dihedral : 7.001 88.844 4434 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.92 % Allowed : 13.03 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3036 helix: 1.12 (0.21), residues: 693 sheet: 0.70 (0.19), residues: 744 loop : -1.58 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 868 HIS 0.008 0.002 HIS A1046 PHE 0.026 0.002 PHE C 888 TYR 0.025 0.002 TYR A 352 ARG 0.006 0.001 ARG B1021 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 152 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7407 (mt) REVERT: A 333 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7869 (pptt) REVERT: B 37 MET cc_start: 0.6927 (mtp) cc_final: 0.6647 (mtm) REVERT: B 421 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8783 (pt) REVERT: B 941 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8253 (mp) REVERT: C 53 TYR cc_start: 0.8067 (t80) cc_final: 0.7823 (t80) REVERT: C 151 MET cc_start: 0.3676 (OUTLIER) cc_final: 0.2671 (ptp) REVERT: C 687 ILE cc_start: 0.8708 (pt) cc_final: 0.8445 (pt) REVERT: C 850 ASP cc_start: 0.7595 (m-30) cc_final: 0.7378 (m-30) outliers start: 78 outliers final: 41 residues processed: 213 average time/residue: 0.9746 time to fit residues: 256.0278 Evaluate side-chains 193 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 296 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 137 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN A 883 GLN B 546 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25446 Z= 0.223 Angle : 0.548 6.975 34611 Z= 0.288 Chirality : 0.045 0.316 4032 Planarity : 0.005 0.091 4404 Dihedral : 6.654 81.678 4434 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.70 % Allowed : 14.38 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3036 helix: 1.55 (0.22), residues: 666 sheet: 0.75 (0.19), residues: 747 loop : -1.41 (0.14), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 868 HIS 0.005 0.001 HIS A1046 PHE 0.012 0.001 PHE B 83 TYR 0.021 0.001 TYR C 352 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 150 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7359 (mt) REVERT: B 32 GLN cc_start: 0.7347 (mp-120) cc_final: 0.6999 (mp10) REVERT: B 37 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6557 (mtm) REVERT: C 32 GLN cc_start: 0.7534 (mp-120) cc_final: 0.7258 (mp10) REVERT: C 53 TYR cc_start: 0.7980 (t80) cc_final: 0.7715 (t80) REVERT: C 151 MET cc_start: 0.3582 (OUTLIER) cc_final: 0.2730 (ptp) REVERT: C 687 ILE cc_start: 0.8679 (pt) cc_final: 0.8423 (pt) outliers start: 72 outliers final: 49 residues processed: 205 average time/residue: 0.9501 time to fit residues: 240.1846 Evaluate side-chains 196 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 144 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Chi-restraints excluded: chain C residue 1099 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN B 546 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25446 Z= 0.215 Angle : 0.552 9.556 34611 Z= 0.289 Chirality : 0.045 0.315 4032 Planarity : 0.004 0.090 4404 Dihedral : 6.541 75.152 4434 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.73 % Allowed : 14.72 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3036 helix: 1.49 (0.21), residues: 690 sheet: 0.80 (0.19), residues: 747 loop : -1.43 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 868 HIS 0.004 0.001 HIS B1046 PHE 0.013 0.001 PHE C 379 TYR 0.021 0.001 TYR A 352 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 147 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7523 (mp-120) cc_final: 0.7294 (mp10) REVERT: A 264 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7349 (mt) REVERT: A 333 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7893 (pttp) REVERT: A 551 PHE cc_start: 0.6276 (OUTLIER) cc_final: 0.5289 (p90) REVERT: B 37 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6570 (mtm) REVERT: C 53 TYR cc_start: 0.7986 (t80) cc_final: 0.7756 (t80) REVERT: C 151 MET cc_start: 0.3443 (OUTLIER) cc_final: 0.2601 (ptp) REVERT: C 836 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7106 (ttpp) outliers start: 73 outliers final: 52 residues processed: 200 average time/residue: 0.9490 time to fit residues: 232.4816 Evaluate side-chains 200 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 142 time to evaluate : 2.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 713 MET Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 772 LYS Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 187 optimal weight: 4.9990 chunk 200 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN B 546 GLN B 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25446 Z= 0.336 Angle : 0.608 8.733 34611 Z= 0.319 Chirality : 0.047 0.324 4032 Planarity : 0.005 0.091 4404 Dihedral : 6.660 64.343 4434 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.88 % Allowed : 15.06 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3036 helix: 1.26 (0.21), residues: 696 sheet: 0.76 (0.19), residues: 744 loop : -1.54 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 868 HIS 0.007 0.001 HIS A1046 PHE 0.017 0.002 PHE C 83 TYR 0.025 0.002 TYR A 352 ARG 0.004 0.000 ARG A1021 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 149 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7351 (mt) REVERT: A 333 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (pttp) REVERT: A 551 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5350 (p90) REVERT: B 32 GLN cc_start: 0.7445 (mp-120) cc_final: 0.7163 (mp10) REVERT: B 37 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6581 (mtm) REVERT: C 32 GLN cc_start: 0.7501 (mp-120) cc_final: 0.7293 (mp10) REVERT: C 53 TYR cc_start: 0.8081 (t80) cc_final: 0.7801 (t80) REVERT: C 56 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7228 (pt0) REVERT: C 151 MET cc_start: 0.3585 (OUTLIER) cc_final: 0.2587 (ptp) REVERT: C 687 ILE cc_start: 0.8713 (pt) cc_final: 0.8501 (pt) REVERT: C 836 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7172 (ttpp) outliers start: 77 outliers final: 54 residues processed: 208 average time/residue: 0.9686 time to fit residues: 247.7661 Evaluate side-chains 202 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 141 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 181 HIS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 967 CYS Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1054 GLU Chi-restraints excluded: chain B residue 1123 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 220 PHE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 713 MET Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 836 LYS Chi-restraints excluded: chain C residue 901 ASN Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.5980 chunk 257 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 248 optimal weight: 0.6980 chunk 259 optimal weight: 0.0020 chunk 273 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 733 ASN B 546 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 25446 Z= 0.144 Angle : 0.520 9.238 34611 Z= 0.273 Chirality : 0.044 0.301 4032 Planarity : 0.004 0.091 4404 Dihedral : 6.248 58.287 4434 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 15.81 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3036 helix: 2.10 (0.22), residues: 642 sheet: 0.85 (0.20), residues: 744 loop : -1.32 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 868 HIS 0.003 0.001 HIS B1046 PHE 0.010 0.001 PHE B1103 TYR 0.020 0.001 TYR C1049 ARG 0.003 0.000 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 141 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7372 (mt) REVERT: A 333 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7908 (pttp) REVERT: A 551 PHE cc_start: 0.6366 (OUTLIER) cc_final: 0.5300 (p90) REVERT: B 32 GLN cc_start: 0.7383 (mp-120) cc_final: 0.7025 (mp10) REVERT: B 37 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6519 (mtm) REVERT: B 132 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7458 (mm) REVERT: C 32 GLN cc_start: 0.7427 (mp-120) cc_final: 0.7215 (mp10) REVERT: C 56 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7179 (pt0) outliers start: 63 outliers final: 34 residues processed: 191 average time/residue: 0.9444 time to fit residues: 221.9824 Evaluate side-chains 176 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 136 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 762 GLU Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 0.0040 chunk 177 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 242 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 ASN B 546 GLN B 733 ASN ** B 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25446 Z= 0.173 Angle : 0.525 8.696 34611 Z= 0.276 Chirality : 0.044 0.308 4032 Planarity : 0.004 0.091 4404 Dihedral : 6.180 56.008 4434 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.95 % Allowed : 16.48 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 3036 helix: 1.85 (0.21), residues: 672 sheet: 0.84 (0.20), residues: 744 loop : -1.31 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 868 HIS 0.004 0.001 HIS B1046 PHE 0.011 0.001 PHE B1103 TYR 0.020 0.001 TYR A 352 ARG 0.007 0.000 ARG B 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 138 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7378 (mt) REVERT: A 551 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5327 (p90) REVERT: B 32 GLN cc_start: 0.7384 (mp-120) cc_final: 0.7033 (mp10) REVERT: B 37 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6501 (mtm) REVERT: B 132 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7473 (mm) REVERT: C 32 GLN cc_start: 0.7427 (mp-120) cc_final: 0.7133 (mp10) REVERT: C 56 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7192 (pt0) REVERT: C 151 MET cc_start: 0.3578 (OUTLIER) cc_final: 0.2321 (ptp) outliers start: 52 outliers final: 36 residues processed: 183 average time/residue: 0.9976 time to fit residues: 225.0950 Evaluate side-chains 178 residues out of total 2670 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 551 PHE Chi-restraints excluded: chain A residue 967 CYS Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 181 HIS Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 901 ASN Chi-restraints excluded: chain B residue 1032 MET Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 369 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 772 LYS Chi-restraints excluded: chain C residue 967 CYS Chi-restraints excluded: chain C residue 1047 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.0170 chunk 74 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: