Starting phenix.real_space_refine on Sat Aug 10 20:54:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukl_26583/08_2024/7ukl_26583.cif" } resolution = 3.09 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= 0.040 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 132 5.16 5 C 19197 2.51 5 N 4965 2.21 5 O 5940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "X PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 95": "OD1" <-> "OD2" Residue "X TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 101": "OD1" <-> "OD2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 287": "OD1" <-> "OD2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C ASP 994": "OD1" <-> "OD2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C ASP 1139": "OD1" <-> "OD2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 53": "OD1" <-> "OD2" Residue "M PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30234 Number of models: 1 Model: "" Number of chains: 12 Chain: "Y" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "X" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "A" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8004 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "M" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1030 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 128} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 820 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "B" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Chain: "A" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 16.17, per 1000 atoms: 0.53 Number of scatterers: 30234 At special positions: 0 Unit cell: (177.62, 172.64, 171.81, 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 132 16.00 O 5940 8.00 N 4965 7.00 C 19197 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.09 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A 717 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A 122 " " NAG A1313 " - " ASN A 61 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 165 " " NAG A1316 " - " ASN A 343 " " NAG B1301 " - " ASN B 657 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B1134 " " NAG B1306 " - " ASN B1098 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 603 " " NAG B1313 " - " ASN B 616 " " NAG B1314 " - " ASN B 343 " " NAG B1315 " - " ASN B 331 " " NAG B1316 " - " ASN B 122 " " NAG C1301 " - " ASN C 616 " " NAG C1302 " - " ASN C 657 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C1134 " " NAG C1311 " - " ASN C 122 " " NAG C1312 " - " ASN C 61 " " NAG C1313 " - " ASN C 234 " " NAG C1314 " - " ASN C 165 " " NAG C1315 " - " ASN C 603 " " NAG C1316 " - " ASN C 343 " Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 5.0 seconds 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 57 sheets defined 22.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'Y' and resid 27 through 31 Processing helix chain 'Y' and resid 79 through 83 removed outlier: 4.129A pdb=" N GLU Y 83 " --> pdb=" O ALA Y 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.599A pdb=" N GLN B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.791A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.794A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.635A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.521A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.589A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.821A pdb=" N VAL B 622 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.797A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.517A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.547A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.507A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.523A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.662A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.947A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 32 Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.963A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.786A pdb=" N LYS C 182 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.666A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.639A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.611A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 623 removed outlier: 3.548A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.519A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.675A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.701A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.548A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.012A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.916A pdb=" N GLN A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.647A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.709A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.604A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.605A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.653A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.351A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'N' and resid 92 through 95A removed outlier: 3.513A pdb=" N THR N 95 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 9 through 13 removed outlier: 6.609A pdb=" N VAL Y 11 " --> pdb=" O THR Y 105 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA Y 84 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP Y 35 " --> pdb=" O VAL Y 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 19 through 24 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 removed outlier: 5.419A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.149A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.873A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.683A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.373A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 removed outlier: 5.211A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.534A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 543 removed outlier: 4.046A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.154A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.987A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.987A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.409A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.711A pdb=" N ILE B 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.806A pdb=" N MET X 34 " --> pdb=" O ILE X 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ILE X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.457A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.548A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.159A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.995A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.740A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.605A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 356 through 358 removed outlier: 4.523A pdb=" N VAL C 395 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER C 514 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C 397 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL C 512 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER C 399 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 510 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL C 401 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR C 508 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'C' and resid 538 through 543 removed outlier: 4.918A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE C 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.242A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 701 through 703 Processing sheet with id=AD7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.002A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.002A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.398A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.638A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.031A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.992A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.934A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.141A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.505A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AE9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.110A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.479A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.518A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.811A pdb=" N MET H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.538A pdb=" N THR M 77 " --> pdb=" O ASP M 72 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.923A pdb=" N MET M 34 " --> pdb=" O ILE M 50 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 9 through 13 removed outlier: 6.510A pdb=" N VAL N 11 " --> pdb=" O THR N 105 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TRP N 35 " --> pdb=" O VAL N 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 19 through 24 1189 hydrogen bonds defined for protein. 3108 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: 13.79 Time building geometry restraints manager: 12.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4930 1.32 - 1.45: 8818 1.45 - 1.58: 16996 1.58 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 30912 Sorted by residual: bond pdb=" N CYS A 738 " pdb=" CA CYS A 738 " ideal model delta sigma weight residual 1.459 1.383 0.076 1.21e-02 6.83e+03 3.98e+01 bond pdb=" CA CYS A 738 " pdb=" C CYS A 738 " ideal model delta sigma weight residual 1.523 1.467 0.057 1.30e-02 5.92e+03 1.91e+01 bond pdb=" N VAL C1128 " pdb=" CA VAL C1128 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.06e-02 8.90e+03 1.83e+01 bond pdb=" C SER B 735 " pdb=" O SER B 735 " ideal model delta sigma weight residual 1.234 1.188 0.046 1.11e-02 8.12e+03 1.74e+01 bond pdb=" CA SER A 530 " pdb=" CB SER A 530 " ideal model delta sigma weight residual 1.528 1.477 0.052 1.35e-02 5.49e+03 1.46e+01 ... (remaining 30907 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.67: 908 106.67 - 113.60: 16728 113.60 - 120.53: 12143 120.53 - 127.46: 11994 127.46 - 134.39: 284 Bond angle restraints: 42057 Sorted by residual: angle pdb=" N THR C 747 " pdb=" CA THR C 747 " pdb=" C THR C 747 " ideal model delta sigma weight residual 112.54 101.67 10.87 1.22e+00 6.72e-01 7.93e+01 angle pdb=" N VAL B 126 " pdb=" CA VAL B 126 " pdb=" C VAL B 126 " ideal model delta sigma weight residual 110.05 100.50 9.55 1.09e+00 8.42e-01 7.68e+01 angle pdb=" N PHE C 342 " pdb=" CA PHE C 342 " pdb=" C PHE C 342 " ideal model delta sigma weight residual 111.82 121.48 -9.66 1.16e+00 7.43e-01 6.94e+01 angle pdb=" N THR C 602 " pdb=" CA THR C 602 " pdb=" C THR C 602 " ideal model delta sigma weight residual 111.75 103.22 8.53 1.28e+00 6.10e-01 4.44e+01 angle pdb=" CA VAL A 395 " pdb=" C VAL A 395 " pdb=" O VAL A 395 " ideal model delta sigma weight residual 121.59 115.77 5.82 1.03e+00 9.43e-01 3.19e+01 ... (remaining 42052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 17487 17.58 - 35.16: 1158 35.16 - 52.74: 232 52.74 - 70.32: 63 70.32 - 87.90: 29 Dihedral angle restraints: 18969 sinusoidal: 7968 harmonic: 11001 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 -31.31 -54.69 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -34.95 -51.05 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 150.29 29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 18966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.174: 4788 0.174 - 0.347: 69 0.347 - 0.521: 8 0.521 - 0.694: 0 0.694 - 0.868: 1 Chirality restraints: 4866 Sorted by residual: chirality pdb=" C1 NAG B1316 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1316 " pdb=" O5 NAG B1316 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 801 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA PHE C 318 " pdb=" N PHE C 318 " pdb=" C PHE C 318 " pdb=" CB PHE C 318 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.20e+00 ... (remaining 4863 not shown) Planarity restraints: 5439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1314 " 0.338 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B1314 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1314 " 0.087 2.00e-02 2.50e+03 pdb=" N2 NAG B1314 " -0.522 2.00e-02 2.50e+03 pdb=" O7 NAG B1314 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1311 " 0.342 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG B1311 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B1311 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG B1311 " -0.515 2.00e-02 2.50e+03 pdb=" O7 NAG B1311 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1316 " -0.331 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG A1316 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A1316 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG A1316 " 0.514 2.00e-02 2.50e+03 pdb=" O7 NAG A1316 " -0.141 2.00e-02 2.50e+03 ... (remaining 5436 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 712 2.69 - 3.24: 29428 3.24 - 3.80: 45578 3.80 - 4.35: 64591 4.35 - 4.90: 109211 Nonbonded interactions: 249520 Sorted by model distance: nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.139 3.040 nonbonded pdb=" OD2 ASP M 100A" pdb=" OG1 THR M 100D" model vdw 2.150 3.040 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.164 3.040 nonbonded pdb=" OG SER A 555 " pdb=" O ILE A 584 " model vdw 2.200 3.040 nonbonded pdb=" OD2 ASP A 578 " pdb=" OG1 THR A 581 " model vdw 2.212 3.040 ... (remaining 249515 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.790 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: 0.030 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 79.500 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 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 : 0.005 0.076 30912 Z= 0.349 Angle : 0.865 10.867 42057 Z= 0.549 Chirality : 0.061 0.868 4866 Planarity : 0.015 0.294 5391 Dihedral : 12.695 87.897 11790 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.09 % Allowed : 1.00 % Favored : 98.91 % Cbeta Deviations : 0.09 % 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 (0.14), residues: 3735 helix: 0.71 (0.21), residues: 635 sheet: -0.53 (0.16), residues: 957 loop : -0.53 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 PHE 0.023 0.001 PHE C 515 TYR 0.024 0.001 TYR A 396 ARG 0.005 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 372 time to evaluate : 3.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 37 GLN cc_start: 0.7945 (tt0) cc_final: 0.7722 (tt0) REVERT: Y 82 ASP cc_start: 0.6262 (m-30) cc_final: 0.5943 (m-30) REVERT: C 455 LEU cc_start: 0.8479 (mt) cc_final: 0.8182 (mt) outliers start: 3 outliers final: 2 residues processed: 375 average time/residue: 0.4533 time to fit residues: 263.2760 Evaluate side-chains 255 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 293 optimal weight: 0.0870 chunk 113 optimal weight: 0.2980 chunk 178 optimal weight: 0.6980 chunk 218 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 17 GLN B 164 ASN B 955 ASN ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 388 ASN C 779 GLN A 81 ASN A 207 HIS ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN M 76 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30912 Z= 0.184 Angle : 0.592 9.785 42057 Z= 0.305 Chirality : 0.046 0.257 4866 Planarity : 0.004 0.067 5391 Dihedral : 5.848 58.702 5102 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.03 % Allowed : 6.02 % Favored : 92.95 % 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: -0.23 (0.13), residues: 3735 helix: 1.44 (0.21), residues: 645 sheet: -0.32 (0.16), residues: 932 loop : -0.52 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 35 HIS 0.004 0.001 HIS C 519 PHE 0.024 0.001 PHE B 497 TYR 0.023 0.001 TYR B 453 ARG 0.005 0.000 ARG N 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 3 GLN cc_start: 0.7140 (pm20) cc_final: 0.6355 (pm20) REVERT: N 87 TYR cc_start: 0.7564 (m-80) cc_final: 0.7225 (m-80) outliers start: 34 outliers final: 23 residues processed: 304 average time/residue: 0.4308 time to fit residues: 208.7522 Evaluate side-chains 271 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain M residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 341 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 chunk 303 optimal weight: 2.9990 chunk 338 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 273 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN A 913 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS M 35 HIS N 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30912 Z= 0.192 Angle : 0.557 9.692 42057 Z= 0.287 Chirality : 0.045 0.231 4866 Planarity : 0.004 0.058 5391 Dihedral : 5.496 55.327 5102 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.19 % Allowed : 7.41 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3735 helix: 1.67 (0.21), residues: 658 sheet: -0.16 (0.16), residues: 929 loop : -0.48 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 886 HIS 0.003 0.001 HIS X 35 PHE 0.027 0.001 PHE B 497 TYR 0.028 0.001 TYR B 495 ARG 0.008 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 267 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 82 MET cc_start: 0.6892 (mtm) cc_final: 0.6688 (mtt) REVERT: N 82 ASP cc_start: 0.7488 (m-30) cc_final: 0.7270 (m-30) outliers start: 39 outliers final: 25 residues processed: 289 average time/residue: 0.4936 time to fit residues: 228.6636 Evaluate side-chains 266 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 241 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 162 optimal weight: 0.5980 chunk 229 optimal weight: 0.9980 chunk 342 optimal weight: 8.9990 chunk 362 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 324 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 37 GLN ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 1 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30912 Z= 0.170 Angle : 0.532 9.661 42057 Z= 0.275 Chirality : 0.044 0.233 4866 Planarity : 0.004 0.051 5391 Dihedral : 5.276 55.438 5102 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.43 % Allowed : 8.60 % Favored : 89.97 % 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: 0.09 (0.14), residues: 3735 helix: 1.87 (0.21), residues: 656 sheet: -0.10 (0.16), residues: 927 loop : -0.40 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Y 35 HIS 0.003 0.001 HIS X 35 PHE 0.029 0.001 PHE B 497 TYR 0.022 0.001 TYR B 453 ARG 0.008 0.000 ARG X 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 264 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 81 MET cc_start: 0.8280 (ppp) cc_final: 0.8031 (ppp) REVERT: N 61 ARG cc_start: 0.7667 (ptt90) cc_final: 0.7430 (ptt90) outliers start: 47 outliers final: 32 residues processed: 295 average time/residue: 0.4395 time to fit residues: 205.7132 Evaluate side-chains 266 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain N residue 81 MET Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 269 optimal weight: 0.0570 chunk 149 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 250 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 325 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN ** X 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30912 Z= 0.279 Angle : 0.558 9.610 42057 Z= 0.287 Chirality : 0.045 0.237 4866 Planarity : 0.004 0.049 5391 Dihedral : 5.303 56.841 5102 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.82 % Allowed : 9.30 % Favored : 88.88 % 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: 0.06 (0.14), residues: 3735 helix: 1.87 (0.21), residues: 658 sheet: -0.23 (0.16), residues: 949 loop : -0.37 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 35 HIS 0.004 0.001 HIS C1064 PHE 0.029 0.001 PHE B 497 TYR 0.036 0.001 TYR N 87 ARG 0.008 0.000 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 3.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 67 PHE cc_start: 0.7968 (m-10) cc_final: 0.7714 (m-10) REVERT: L 81 MET cc_start: 0.8364 (ppp) cc_final: 0.8081 (ppp) outliers start: 60 outliers final: 42 residues processed: 293 average time/residue: 0.4260 time to fit residues: 200.3220 Evaluate side-chains 272 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 230 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 81 MET Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 362 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 87 ASN C 196 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30912 Z= 0.201 Angle : 0.542 11.842 42057 Z= 0.277 Chirality : 0.044 0.236 4866 Planarity : 0.004 0.046 5391 Dihedral : 5.227 55.432 5102 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.88 % Allowed : 9.63 % Favored : 88.48 % 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: 0.13 (0.14), residues: 3735 helix: 1.99 (0.21), residues: 660 sheet: -0.22 (0.16), residues: 952 loop : -0.33 (0.14), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Y 35 HIS 0.002 0.001 HIS X 35 PHE 0.028 0.001 PHE B 497 TYR 0.044 0.001 TYR N 87 ARG 0.008 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 245 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 67 PHE cc_start: 0.7867 (m-10) cc_final: 0.7619 (m-10) outliers start: 62 outliers final: 48 residues processed: 288 average time/residue: 0.4159 time to fit residues: 192.0242 Evaluate side-chains 280 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 232 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 206 optimal weight: 0.0770 chunk 264 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 361 optimal weight: 7.9990 chunk 226 optimal weight: 4.9990 chunk 220 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 30912 Z= 0.163 Angle : 0.531 11.510 42057 Z= 0.273 Chirality : 0.044 0.237 4866 Planarity : 0.004 0.045 5391 Dihedral : 5.113 55.364 5102 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 10.27 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.14), residues: 3735 helix: 2.10 (0.21), residues: 660 sheet: -0.13 (0.16), residues: 956 loop : -0.29 (0.14), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.002 0.000 HIS B1048 PHE 0.030 0.001 PHE B 497 TYR 0.033 0.001 TYR N 87 ARG 0.008 0.000 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 256 time to evaluate : 3.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 1 GLN cc_start: 0.7377 (tm-30) cc_final: 0.6919 (tm-30) REVERT: X 67 PHE cc_start: 0.7827 (m-10) cc_final: 0.7591 (m-10) outliers start: 63 outliers final: 51 residues processed: 297 average time/residue: 0.4282 time to fit residues: 203.9095 Evaluate side-chains 288 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 178 optimal weight: 0.2980 chunk 33 optimal weight: 0.5980 chunk 284 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 360 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30912 Z= 0.160 Angle : 0.540 12.414 42057 Z= 0.276 Chirality : 0.044 0.250 4866 Planarity : 0.004 0.044 5391 Dihedral : 5.054 55.398 5102 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.79 % Allowed : 10.85 % Favored : 87.36 % 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: 0.26 (0.14), residues: 3735 helix: 2.16 (0.21), residues: 660 sheet: -0.14 (0.16), residues: 953 loop : -0.26 (0.14), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.002 0.000 HIS X 35 PHE 0.040 0.001 PHE B 497 TYR 0.029 0.001 TYR N 87 ARG 0.008 0.000 ARG B 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 250 time to evaluate : 3.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 1 GLN cc_start: 0.7364 (tm-30) cc_final: 0.6974 (tm-30) outliers start: 59 outliers final: 54 residues processed: 286 average time/residue: 0.4267 time to fit residues: 197.7416 Evaluate side-chains 288 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 234 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 3.9990 chunk 346 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 146 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 103 optimal weight: 0.0980 chunk 304 optimal weight: 0.7980 chunk 318 optimal weight: 3.9990 chunk 335 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN B 422 ASN C 856 ASN C 901 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30912 Z= 0.170 Angle : 0.544 11.412 42057 Z= 0.278 Chirality : 0.044 0.238 4866 Planarity : 0.004 0.043 5391 Dihedral : 5.014 55.475 5102 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.76 % Allowed : 11.30 % Favored : 86.93 % 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: 0.30 (0.14), residues: 3735 helix: 2.20 (0.21), residues: 660 sheet: -0.11 (0.16), residues: 964 loop : -0.25 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 886 HIS 0.003 0.001 HIS B1048 PHE 0.037 0.001 PHE B 497 TYR 0.028 0.001 TYR A 495 ARG 0.010 0.000 ARG M 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 251 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 54 residues processed: 286 average time/residue: 0.4308 time to fit residues: 197.8751 Evaluate side-chains 292 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 238 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 20 LEU Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 30 ASP Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 3.9990 chunk 356 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 373 optimal weight: 9.9990 chunk 343 optimal weight: 0.8980 chunk 297 optimal weight: 0.0030 chunk 30 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 ASN C 173 GLN A 901 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30912 Z= 0.213 Angle : 0.566 12.643 42057 Z= 0.289 Chirality : 0.044 0.237 4866 Planarity : 0.004 0.043 5391 Dihedral : 5.067 55.606 5102 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.64 % Allowed : 11.67 % Favored : 86.69 % 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: 0.30 (0.14), residues: 3735 helix: 2.22 (0.21), residues: 660 sheet: -0.09 (0.16), residues: 941 loop : -0.26 (0.14), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 886 HIS 0.009 0.001 HIS H 35 PHE 0.041 0.001 PHE A 497 TYR 0.045 0.001 TYR N 87 ARG 0.009 0.000 ARG M 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 240 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 50 residues processed: 274 average time/residue: 0.4226 time to fit residues: 190.4746 Evaluate side-chains 278 residues out of total 3291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 228 time to evaluate : 3.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 48 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 361 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain X residue 108 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.9792 > 50: distance: 23 - 111: 28.536 distance: 98 - 100: 10.503 distance: 100 - 101: 22.089 distance: 101 - 102: 34.290 distance: 101 - 104: 21.861 distance: 102 - 103: 22.805 distance: 102 - 108: 23.714 distance: 104 - 105: 7.705 distance: 104 - 106: 12.418 distance: 105 - 107: 3.684 distance: 108 - 109: 29.319 distance: 109 - 110: 14.452 distance: 109 - 112: 45.721 distance: 110 - 111: 35.891 distance: 110 - 115: 8.704 distance: 112 - 114: 27.228 distance: 115 - 116: 11.757 distance: 116 - 117: 20.540 distance: 116 - 119: 22.472 distance: 117 - 118: 20.010 distance: 117 - 123: 15.440 distance: 119 - 120: 10.623 distance: 120 - 121: 10.563 distance: 120 - 122: 10.973 distance: 122 - 209: 10.301 distance: 123 - 124: 11.210 distance: 124 - 125: 14.043 distance: 124 - 127: 13.050 distance: 125 - 126: 18.870 distance: 125 - 131: 11.328 distance: 128 - 129: 5.383 distance: 128 - 130: 3.541 distance: 131 - 132: 20.989 distance: 132 - 133: 26.184 distance: 132 - 135: 27.467 distance: 133 - 134: 16.973 distance: 133 - 138: 28.106 distance: 135 - 136: 10.931 distance: 135 - 137: 18.269 distance: 138 - 139: 11.788 distance: 139 - 140: 12.641 distance: 139 - 142: 16.408 distance: 140 - 141: 7.730 distance: 140 - 145: 12.612 distance: 142 - 143: 5.551 distance: 142 - 144: 31.897 distance: 145 - 146: 18.926 distance: 146 - 147: 13.652 distance: 146 - 149: 17.636 distance: 147 - 148: 9.910 distance: 147 - 157: 35.575 distance: 149 - 150: 4.225 distance: 150 - 151: 12.009 distance: 150 - 152: 30.824 distance: 151 - 153: 6.283 distance: 152 - 154: 22.236 distance: 153 - 155: 33.469 distance: 154 - 155: 20.493 distance: 155 - 156: 15.958 distance: 157 - 158: 29.883 distance: 158 - 159: 26.130 distance: 158 - 161: 43.638 distance: 159 - 160: 11.121 distance: 159 - 165: 20.249 distance: 161 - 162: 15.139 distance: 162 - 163: 10.015 distance: 162 - 164: 20.988 distance: 165 - 166: 4.313 distance: 165 - 171: 22.099 distance: 166 - 167: 8.142 distance: 166 - 169: 42.929 distance: 167 - 168: 33.410 distance: 167 - 172: 25.107 distance: 169 - 170: 7.973 distance: 170 - 171: 38.460 distance: 173 - 174: 24.125 distance: 173 - 176: 29.505 distance: 174 - 175: 35.533 distance: 174 - 180: 17.459 distance: 176 - 177: 20.627 distance: 177 - 178: 36.188 distance: 177 - 179: 4.253