Starting phenix.real_space_refine on Wed Mar 20 19:17:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wt7_32770/03_2024/7wt7_32770.pdb" } resolution = 3.4 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= -0.002 sd= 0.078 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 125 5.16 5 C 18053 2.51 5 N 4654 2.21 5 O 5490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 772": "OD1" <-> "OD2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B GLU 551": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B TYR 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 566": "OD1" <-> "OD2" Residue "C GLU 656": "OE1" <-> "OE2" Residue "C TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 983": "OE1" <-> "OE2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 50": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28322 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8630 Classifications: {'peptide': 1098} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 900 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 831 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 14.73, per 1000 atoms: 0.52 Number of scatterers: 28322 At special positions: 0 Unit cell: (142.31, 144.45, 242.89, 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 125 16.00 O 5490 8.00 N 4654 7.00 C 18053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.05 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.05 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 286 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 356 " distance=2.02 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 520 " distance=2.03 Simple disulfide: pdb=" SG CYS C 475 " - pdb=" SG CYS C 483 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 657 " - pdb=" SG CYS C 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 733 " - pdb=" SG CYS C 755 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 744 " distance=2.03 Simple disulfide: pdb=" SG CYS C1027 " - pdb=" SG CYS C1038 " distance=2.03 Simple disulfide: pdb=" SG CYS C1077 " - pdb=" SG CYS C1121 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 340 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 233 " " NAG A1306 " - " ASN A 600 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 714 " " NAG A1310 " - " ASN A1071 " " NAG A1311 " - " ASN A 798 " " NAG A1312 " - " ASN A 706 " " NAG B1301 " - " ASN B1071 " " NAG B1302 " - " ASN B 714 " " NAG B1303 " - " ASN B 798 " " NAG B1304 " - " ASN B 706 " " NAG B1305 " - " ASN B1095 " " NAG B1306 " - " ASN B1131 " " NAG B1307 " - " ASN B 125 " " NAG B1308 " - " ASN B 145 " " NAG B1309 " - " ASN B 17 " " NAG B1310 " - " ASN B 340 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 233 " " NAG B1313 " - " ASN B 600 " " NAG B1314 " - " ASN B 328 " " NAG B1315 " - " ASN B 613 " " NAG C1301 " - " ASN C 326 " " NAG C1302 " - " ASN C 338 " " NAG C1303 " - " ASN C 598 " " NAG C1304 " - " ASN C 611 " " NAG C1305 " - " ASN C 704 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 145 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 233 " " NAG C1311 " - " ASN C 652 " " NAG C1312 " - " ASN C1069 " " NAG C1313 " - " ASN C1093 " " NAG C1314 " - " ASN C1129 " " NAG E 1 " - " ASN A1095 " " NAG F 1 " - " ASN A1131 " " NAG G 1 " - " ASN C 712 " " NAG I 1 " - " ASN C 796 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 5.1 seconds 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 56 sheets defined 24.0% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.21 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 362 through 368 Processing helix chain 'A' and resid 380 through 386 removed outlier: 4.546A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.799A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 removed outlier: 4.087A pdb=" N ALA A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.962A pdb=" N THR A 824 " --> pdb=" O PHE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 851 Processing helix chain 'A' and resid 863 through 878 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.519A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 904 removed outlier: 3.578A pdb=" N ALA A 900 " --> pdb=" O PRO A 896 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 904 " --> pdb=" O ALA A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.766A pdb=" N ILE A 920 " --> pdb=" O ASN A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.405A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1158 removed outlier: 4.960A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU A1148 " --> pdb=" O SER A1144 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.608A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.519A pdb=" N TRP B 350 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.798A pdb=" N LEU B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 removed outlier: 4.393A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.833A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 630 through 636 removed outlier: 3.585A pdb=" N THR B 635 " --> pdb=" O VAL B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 743 through 754 removed outlier: 4.087A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 780 removed outlier: 3.984A pdb=" N THR B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 766 " --> pdb=" O ARG B 762 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 878 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 898 Processing helix chain 'B' and resid 902 through 907 removed outlier: 3.636A pdb=" N ILE B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 938 removed outlier: 4.007A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS B 918 " --> pdb=" O TYR B 914 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 919 " --> pdb=" O GLU B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 960 removed outlier: 3.546A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 965 removed outlier: 3.806A pdb=" N SER B 964 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 965 " --> pdb=" O GLN B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 961 through 965' Processing helix chain 'B' and resid 973 through 980 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.102A pdb=" N GLU B 987 " --> pdb=" O PRO B 983 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B1022 " --> pdb=" O SER B1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1158 removed outlier: 4.434A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 332 through 338 removed outlier: 3.675A pdb=" N VAL C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 removed outlier: 3.710A pdb=" N TYR C 364 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 382 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 412 through 417 Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 620 through 624 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.582A pdb=" N ASN C 746 " --> pdb=" O THR C 742 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 749 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 750 " --> pdb=" O ASN C 746 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C 751 " --> pdb=" O LEU C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 778 removed outlier: 3.776A pdb=" N ALA C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLN C 774 " --> pdb=" O ASP C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 821 Processing helix chain 'C' and resid 844 through 849 Processing helix chain 'C' and resid 861 through 877 Processing helix chain 'C' and resid 881 through 885 Processing helix chain 'C' and resid 892 through 897 Processing helix chain 'C' and resid 898 through 900 No H-bonds generated for 'chain 'C' and resid 898 through 900' Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 910 through 936 removed outlier: 4.616A pdb=" N LYS C 916 " --> pdb=" O TYR C 912 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU C 917 " --> pdb=" O GLU C 913 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN C 930 " --> pdb=" O ILE C 926 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP C 931 " --> pdb=" O GLY C 927 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C 934 " --> pdb=" O GLN C 930 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 936 " --> pdb=" O SER C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 939 No H-bonds generated for 'chain 'C' and resid 937 through 939' Processing helix chain 'C' and resid 940 through 960 removed outlier: 3.581A pdb=" N VAL C 946 " --> pdb=" O LYS C 942 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 963 No H-bonds generated for 'chain 'C' and resid 961 through 963' Processing helix chain 'C' and resid 971 through 979 Processing helix chain 'C' and resid 980 through 1027 removed outlier: 3.670A pdb=" N ARG C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 991 " --> pdb=" O GLN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1135 through 1156 removed outlier: 4.013A pdb=" N PHE C1143 " --> pdb=" O GLU C1139 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU C1146 " --> pdb=" O SER C1142 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C1148 " --> pdb=" O LYS C1144 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS C1149 " --> pdb=" O GLU C1145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS C1152 " --> pdb=" O ASP C1148 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C1153 " --> pdb=" O LYS C1149 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.919A pdb=" N ILE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.744A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 261 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 226 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.549A pdb=" N PHE A 43 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.661A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 11.777A pdb=" N VAL A 126 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 10.339A pdb=" N GLU A 166 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N ILE A 128 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N THR A 164 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL A 130 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN A 162 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 132 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA A 160 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLN A 134 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.606A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 592 " --> pdb=" O SER A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.299A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 324 removed outlier: 4.299A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 550 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.755A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 355 " --> pdb=" O VAL A 392 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 433 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 508 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 388 through 389 removed outlier: 4.082A pdb=" N VAL A 521 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 607 through 609 removed outlier: 3.564A pdb=" N TYR A 609 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLY A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.115A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.756A pdb=" N ASN A 700 " --> pdb=" O LYS C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 717 removed outlier: 6.132A pdb=" N PHE A 715 " --> pdb=" O PRO A1066 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE A 717 " --> pdb=" O TYR A1064 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A1064 " --> pdb=" O ILE A 717 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A1044 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 720 through 725 Processing sheet with id=AB8, first strand: chain 'A' and resid 731 through 732 removed outlier: 3.514A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1086 through 1087 Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.578A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA B 261 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.985A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.913A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 126 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 168 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 128 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLU B 166 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 130 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 311 removed outlier: 3.578A pdb=" N GLY B 308 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 315 through 316 removed outlier: 3.522A pdb=" N GLY B 590 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.756A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU B 513 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.963A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 535 through 539 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.219A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AD4, first strand: chain 'B' and resid 715 through 719 removed outlier: 6.846A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 722 through 725 removed outlier: 3.736A pdb=" N GLU B 722 " --> pdb=" O PHE B1059 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B1053 " --> pdb=" O GLY B1056 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AD7, first strand: chain 'B' and resid 1078 through 1079 removed outlier: 3.591A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1086 through 1087 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.601A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ASN C 61 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N TYR C 264 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 259 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN C 185 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N HIS C 204 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N LEU C 222 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 36 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.778A pdb=" N ASP C 282 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.022A pdb=" N ILE C 105 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C 126 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 168 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 128 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU C 166 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 130 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU C 132 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN C 162 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N GLN C 134 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA C 160 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 306 through 307 removed outlier: 3.526A pdb=" N THR C 594 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE C 638 " --> pdb=" O LEU C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 349 through 352 removed outlier: 3.756A pdb=" N TRP C 431 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 349 through 352 removed outlier: 5.133A pdb=" N ASN C 389 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU C 511 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 447 through 449 Processing sheet with id=AE7, first strand: chain 'C' and resid 468 through 469 Processing sheet with id=AE8, first strand: chain 'C' and resid 533 through 534 Processing sheet with id=AE9, first strand: chain 'C' and resid 537 through 538 removed outlier: 3.531A pdb=" N PHE C 538 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 649 through 650 removed outlier: 5.801A pdb=" N GLU C 649 " --> pdb=" O ALA C 689 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR C 691 " --> pdb=" O GLU C 649 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 706 through 710 Processing sheet with id=AF3, first strand: chain 'C' and resid 713 through 717 removed outlier: 3.701A pdb=" N GLU C 720 " --> pdb=" O PHE C1057 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 717 removed outlier: 7.358A pdb=" N GLY C1054 " --> pdb=" O SER C1050 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER C1050 " --> pdb=" O GLY C1054 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C1056 " --> pdb=" O PRO C1048 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU C1058 " --> pdb=" O SER C1046 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C1046 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL C1060 " --> pdb=" O LEU C1044 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1115 through 1117 removed outlier: 4.236A pdb=" N CYS C1077 " --> pdb=" O VAL C1128 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1089 through 1092 Processing sheet with id=AF7, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.677A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLY H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY H 44 " --> pdb=" O GLY H 40 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.744A pdb=" N THR D 74 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.567A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 45 through 46 966 hydrogen bonds defined for protein. 2580 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.25 Time building geometry restraints manager: 12.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4576 1.30 - 1.44: 8124 1.44 - 1.57: 16125 1.57 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 28984 Sorted by residual: bond pdb=" C PRO B 894 " pdb=" O PRO B 894 " ideal model delta sigma weight residual 1.233 1.167 0.065 1.16e-02 7.43e+03 3.17e+01 bond pdb=" C PRO C 892 " pdb=" O PRO C 892 " ideal model delta sigma weight residual 1.233 1.166 0.067 1.24e-02 6.50e+03 2.89e+01 bond pdb=" C MET B1047 " pdb=" O MET B1047 " ideal model delta sigma weight residual 1.237 1.188 0.049 9.40e-03 1.13e+04 2.76e+01 bond pdb=" CA SER A 813 " pdb=" CB SER A 813 " ideal model delta sigma weight residual 1.530 1.453 0.076 1.57e-02 4.06e+03 2.36e+01 bond pdb=" C PRO A 894 " pdb=" O PRO A 894 " ideal model delta sigma weight residual 1.233 1.169 0.064 1.39e-02 5.18e+03 2.15e+01 ... (remaining 28979 not shown) Histogram of bond angle deviations from ideal: 93.79 - 101.88: 69 101.88 - 109.96: 4557 109.96 - 118.05: 17571 118.05 - 126.14: 16889 126.14 - 134.23: 352 Bond angle restraints: 39438 Sorted by residual: angle pdb=" N PRO A 894 " pdb=" CA PRO A 894 " pdb=" CB PRO A 894 " ideal model delta sigma weight residual 103.19 93.79 9.40 9.00e-01 1.23e+00 1.09e+02 angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.25 94.82 8.43 8.80e-01 1.29e+00 9.18e+01 angle pdb=" C PRO A 894 " pdb=" CA PRO A 894 " pdb=" CB PRO A 894 " ideal model delta sigma weight residual 111.64 100.46 11.18 1.27e+00 6.20e-01 7.75e+01 angle pdb=" N PRO A 983 " pdb=" CA PRO A 983 " pdb=" C PRO A 983 " ideal model delta sigma weight residual 110.70 120.80 -10.10 1.22e+00 6.72e-01 6.85e+01 angle pdb=" N PRO A 896 " pdb=" CA PRO A 896 " pdb=" C PRO A 896 " ideal model delta sigma weight residual 113.47 102.39 11.08 1.43e+00 4.89e-01 6.00e+01 ... (remaining 39433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.81: 16685 21.81 - 43.62: 1059 43.62 - 65.42: 171 65.42 - 87.23: 34 87.23 - 109.04: 17 Dihedral angle restraints: 17966 sinusoidal: 7693 harmonic: 10273 Sorted by residual: dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual -180.00 -132.10 -47.90 0 5.00e+00 4.00e-02 9.18e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -2.18 -83.82 1 1.00e+01 1.00e-02 8.57e+01 dihedral pdb=" CA ASN A 145 " pdb=" C ASN A 145 " pdb=" N ASN A 146 " pdb=" CA ASN A 146 " ideal model delta harmonic sigma weight residual -180.00 -136.79 -43.21 0 5.00e+00 4.00e-02 7.47e+01 ... (remaining 17963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 4521 0.184 - 0.367: 59 0.367 - 0.551: 6 0.551 - 0.734: 0 0.734 - 0.918: 1 Chirality restraints: 4587 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA TYR C 912 " pdb=" N TYR C 912 " pdb=" C TYR C 912 " pdb=" CB TYR C 912 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.50e+00 chirality pdb=" CA ASN B 146 " pdb=" N ASN B 146 " pdb=" C ASN B 146 " pdb=" CB ASN B 146 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.63e+00 ... (remaining 4584 not shown) Planarity restraints: 5081 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 937 " -0.030 2.00e-02 2.50e+03 6.12e-02 3.75e+01 pdb=" C SER A 937 " 0.106 2.00e-02 2.50e+03 pdb=" O SER A 937 " -0.040 2.00e-02 2.50e+03 pdb=" N THR A 938 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 911 " 0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" C ASN A 911 " -0.099 2.00e-02 2.50e+03 pdb=" O ASN A 911 " 0.038 2.00e-02 2.50e+03 pdb=" N VAL A 912 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 617 " 0.097 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 618 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " 0.076 5.00e-02 4.00e+02 ... (remaining 5078 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 783 2.69 - 3.24: 27681 3.24 - 3.79: 41018 3.79 - 4.35: 54071 4.35 - 4.90: 90489 Nonbonded interactions: 214042 Sorted by model distance: nonbonded pdb=" OH TYR C 669 " pdb=" OE1 GLN C 685 " model vdw 2.132 2.440 nonbonded pdb=" O GLY A 877 " pdb=" OG SER A 881 " model vdw 2.145 2.440 nonbonded pdb=" OG SER A 98 " pdb=" O GLU A 177 " model vdw 2.162 2.440 nonbonded pdb=" OD1 ASN B 706 " pdb=" ND2 ASN B 707 " model vdw 2.166 2.520 nonbonded pdb=" O GLY C 875 " pdb=" OG SER C 879 " model vdw 2.197 2.440 ... (remaining 214037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 442 or (resid 443 through 444 and (name N or na \ me CA or name C or name O )) or resid 445 through 1159 or resid 1301 through 131 \ 2)) selection = (chain 'B' and (resid 14 through 442 or (resid 443 through 444 and (name N or na \ me CA or name C or name O )) or resid 445 through 1159 or resid 1301 through 131 \ 2)) selection = (chain 'C' and (resid 14 through 1157 or resid 1301 through 1312)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 11.510 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 75.410 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 95.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 28984 Z= 0.354 Angle : 0.924 12.792 39438 Z= 0.586 Chirality : 0.059 0.918 4587 Planarity : 0.006 0.141 5036 Dihedral : 14.356 109.040 11233 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.11 % Favored : 92.61 % Rotamer: Outliers : 0.91 % Allowed : 1.16 % Favored : 97.93 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.13), residues: 3489 helix: -0.31 (0.19), residues: 709 sheet: -0.57 (0.19), residues: 709 loop : -1.80 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 36 HIS 0.005 0.001 HIS B 143 PHE 0.034 0.002 PHE B 133 TYR 0.024 0.001 TYR B 633 ARG 0.007 0.000 ARG A 405 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 262 time to evaluate : 3.176 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: B 147 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6806 (mmtt) REVERT: B 618 PRO cc_start: 0.6448 (Cg_exo) cc_final: 0.6177 (Cg_endo) REVERT: C 447 LEU cc_start: 0.8452 (mp) cc_final: 0.8232 (tt) REVERT: C 820 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8741 (mtpp) REVERT: C 989 ASP cc_start: 0.6797 (m-30) cc_final: 0.5959 (m-30) REVERT: D 42 LYS cc_start: 0.6923 (pptt) cc_final: 0.6056 (pptt) REVERT: D 50 ASP cc_start: 0.8146 (t0) cc_final: 0.7914 (t0) REVERT: D 71 PHE cc_start: 0.7715 (t80) cc_final: 0.7436 (t80) REVERT: D 86 TYR cc_start: 0.6437 (m-10) cc_final: 0.6106 (m-10) outliers start: 28 outliers final: 8 residues processed: 287 average time/residue: 0.3622 time to fit residues: 170.4698 Evaluate side-chains 207 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 3.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain C residue 820 LYS Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 1067 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 8.9990 chunk 264 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 273 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN B 923 GLN B 954 GLN B1002 GLN C 185 ASN C 217 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 757 GLN C 799 GLN C 908 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28984 Z= 0.256 Angle : 0.643 11.221 39438 Z= 0.328 Chirality : 0.048 0.658 4587 Planarity : 0.005 0.094 5036 Dihedral : 8.175 76.825 4859 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.65 % Favored : 93.26 % Rotamer: Outliers : 0.84 % Allowed : 8.21 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.14), residues: 3489 helix: 0.22 (0.19), residues: 732 sheet: -0.50 (0.19), residues: 738 loop : -1.82 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 433 HIS 0.005 0.001 HIS B1156 PHE 0.021 0.002 PHE C 395 TYR 0.023 0.002 TYR A 492 ARG 0.004 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7086 (t80) cc_final: 0.6721 (t80) REVERT: A 362 TYR cc_start: 0.7585 (m-80) cc_final: 0.7372 (m-80) REVERT: C 487 LEU cc_start: 0.7289 (mm) cc_final: 0.6430 (tp) REVERT: C 541 LEU cc_start: 0.8259 (mt) cc_final: 0.7923 (mt) REVERT: H 17 SER cc_start: 0.5040 (OUTLIER) cc_final: 0.4505 (t) REVERT: H 34 MET cc_start: 0.3947 (mmm) cc_final: 0.3727 (mmp) REVERT: H 36 TRP cc_start: 0.3335 (OUTLIER) cc_final: 0.2996 (t-100) REVERT: H 88 GLU cc_start: 0.5557 (pm20) cc_final: 0.5284 (pm20) REVERT: D 71 PHE cc_start: 0.7614 (t80) cc_final: 0.7287 (t80) REVERT: D 98 PHE cc_start: 0.6516 (m-80) cc_final: 0.6115 (m-80) outliers start: 26 outliers final: 16 residues processed: 233 average time/residue: 0.3664 time to fit residues: 141.9869 Evaluate side-chains 201 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 882 THR Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 317 optimal weight: 0.6980 chunk 342 optimal weight: 9.9990 chunk 282 optimal weight: 0.0170 chunk 314 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 254 optimal weight: 4.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 ASN ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 185 ASN C 799 GLN C 908 GLN C 921 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28984 Z= 0.184 Angle : 0.588 10.229 39438 Z= 0.298 Chirality : 0.046 0.640 4587 Planarity : 0.004 0.061 5036 Dihedral : 6.784 56.065 4840 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 1.65 % Allowed : 10.64 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3489 helix: 0.58 (0.19), residues: 746 sheet: -0.45 (0.19), residues: 742 loop : -1.75 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 149 HIS 0.006 0.001 HIS B1156 PHE 0.023 0.001 PHE B 133 TYR 0.024 0.001 TYR C 702 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 212 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 TYR cc_start: 0.7258 (t80) cc_final: 0.6948 (t80) REVERT: A 1106 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: B 884 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (t) REVERT: C 487 LEU cc_start: 0.7239 (mm) cc_final: 0.6369 (tp) REVERT: H 17 SER cc_start: 0.4878 (OUTLIER) cc_final: 0.4071 (t) REVERT: D 42 LYS cc_start: 0.7735 (pptt) cc_final: 0.7205 (mtmm) REVERT: D 86 TYR cc_start: 0.6913 (m-10) cc_final: 0.6682 (m-10) REVERT: D 87 TYR cc_start: 0.6464 (m-80) cc_final: 0.5805 (m-10) outliers start: 51 outliers final: 31 residues processed: 246 average time/residue: 0.3346 time to fit residues: 140.8958 Evaluate side-chains 219 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 318 optimal weight: 2.9990 chunk 337 optimal weight: 30.0000 chunk 166 optimal weight: 4.9990 chunk 301 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 185 ASN C 329 ASN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 GLN C 930 GLN ** C 944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 28984 Z= 0.378 Angle : 0.679 10.897 39438 Z= 0.347 Chirality : 0.049 0.670 4587 Planarity : 0.005 0.054 5036 Dihedral : 6.493 57.109 4839 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.92 % Rotamer: Outliers : 2.72 % Allowed : 13.13 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.14), residues: 3489 helix: 0.16 (0.19), residues: 754 sheet: -0.60 (0.18), residues: 787 loop : -1.86 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 149 HIS 0.007 0.001 HIS B1156 PHE 0.025 0.002 PHE C 901 TYR 0.032 0.002 TYR A 492 ARG 0.004 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 196 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 PHE cc_start: 0.7100 (m-80) cc_final: 0.6757 (m-80) REVERT: A 174 MET cc_start: 0.1573 (mtt) cc_final: 0.1191 (mtt) REVERT: A 797 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7966 (m-10) REVERT: A 1063 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8534 (m) REVERT: A 1106 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: C 487 LEU cc_start: 0.7286 (mm) cc_final: 0.6361 (tp) REVERT: H 17 SER cc_start: 0.5442 (OUTLIER) cc_final: 0.4669 (t) REVERT: H 83 ASN cc_start: 0.7889 (p0) cc_final: 0.7404 (t0) REVERT: H 109 TRP cc_start: 0.5249 (m100) cc_final: 0.4454 (m100) REVERT: D 36 TYR cc_start: 0.7054 (m-80) cc_final: 0.6438 (m-80) REVERT: D 71 PHE cc_start: 0.7594 (t80) cc_final: 0.7230 (t80) REVERT: D 86 TYR cc_start: 0.6976 (m-10) cc_final: 0.6677 (m-10) REVERT: D 87 TYR cc_start: 0.6396 (m-80) cc_final: 0.5768 (m-10) outliers start: 84 outliers final: 54 residues processed: 263 average time/residue: 0.3262 time to fit residues: 147.1566 Evaluate side-chains 240 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 182 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 797 PHE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1063 THR Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 739 ILE Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 995 THR Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 329 ASN Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 4 optimal weight: 0.0470 chunk 251 optimal weight: 0.4980 chunk 139 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 172 optimal weight: 0.7980 chunk 302 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 28984 Z= 0.152 Angle : 0.575 9.301 39438 Z= 0.291 Chirality : 0.046 0.657 4587 Planarity : 0.004 0.053 5036 Dihedral : 5.886 55.647 4839 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.85 % Favored : 94.04 % Rotamer: Outliers : 1.68 % Allowed : 14.49 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.14), residues: 3489 helix: 0.69 (0.20), residues: 739 sheet: -0.44 (0.19), residues: 780 loop : -1.73 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 PHE 0.023 0.001 PHE B 133 TYR 0.021 0.001 TYR C 702 ARG 0.004 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.1189 (mtt) cc_final: 0.0844 (mtt) REVERT: A 1106 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8311 (m-80) REVERT: C 320 SER cc_start: 0.8427 (m) cc_final: 0.8156 (p) REVERT: C 487 LEU cc_start: 0.7115 (mm) cc_final: 0.6191 (tp) REVERT: H 17 SER cc_start: 0.5171 (OUTLIER) cc_final: 0.4439 (t) REVERT: H 83 ASN cc_start: 0.7896 (p0) cc_final: 0.7475 (t0) REVERT: D 71 PHE cc_start: 0.7563 (t80) cc_final: 0.7158 (t80) REVERT: D 86 TYR cc_start: 0.7099 (m-80) cc_final: 0.6794 (m-10) REVERT: D 87 TYR cc_start: 0.6488 (m-80) cc_final: 0.5825 (m-10) outliers start: 52 outliers final: 36 residues processed: 244 average time/residue: 0.3434 time to fit residues: 144.9360 Evaluate side-chains 229 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 4.9990 chunk 303 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 337 optimal weight: 20.0000 chunk 280 optimal weight: 4.9990 chunk 156 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 185 ASN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 28984 Z= 0.328 Angle : 0.633 10.664 39438 Z= 0.322 Chirality : 0.048 0.657 4587 Planarity : 0.005 0.054 5036 Dihedral : 5.986 59.864 4839 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 2.59 % Allowed : 15.17 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3489 helix: 0.48 (0.19), residues: 745 sheet: -0.55 (0.19), residues: 788 loop : -1.81 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 PHE 0.026 0.002 PHE A 589 TYR 0.027 0.002 TYR A 492 ARG 0.003 0.000 ARG C 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 189 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5977 (m-80) cc_final: 0.5627 (m-80) REVERT: A 165 PHE cc_start: 0.7043 (m-80) cc_final: 0.6784 (m-80) REVERT: A 174 MET cc_start: 0.1353 (mtt) cc_final: 0.1020 (mtt) REVERT: B 884 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8675 (t) REVERT: C 487 LEU cc_start: 0.7273 (mm) cc_final: 0.6295 (tp) REVERT: C 913 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7141 (mp0) REVERT: H 17 SER cc_start: 0.5289 (OUTLIER) cc_final: 0.4591 (t) REVERT: H 78 LEU cc_start: 0.6451 (tp) cc_final: 0.5855 (tt) REVERT: H 83 ASN cc_start: 0.7936 (p0) cc_final: 0.7514 (t0) REVERT: D 71 PHE cc_start: 0.7553 (t80) cc_final: 0.7137 (t80) REVERT: D 86 TYR cc_start: 0.7160 (m-80) cc_final: 0.6845 (m-10) REVERT: D 87 TYR cc_start: 0.6254 (m-80) cc_final: 0.5691 (m-10) outliers start: 80 outliers final: 60 residues processed: 251 average time/residue: 0.3295 time to fit residues: 142.8159 Evaluate side-chains 245 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 3.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 603 VAL Chi-restraints excluded: chain C residue 612 CYS Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 246 optimal weight: 0.7980 chunk 191 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 188 optimal weight: 0.4980 chunk 336 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 185 ASN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28984 Z= 0.160 Angle : 0.567 10.094 39438 Z= 0.286 Chirality : 0.044 0.348 4587 Planarity : 0.004 0.054 5036 Dihedral : 5.527 58.937 4839 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 2.10 % Allowed : 15.69 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.14), residues: 3489 helix: 0.79 (0.20), residues: 746 sheet: -0.41 (0.19), residues: 781 loop : -1.73 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP H 36 HIS 0.007 0.001 HIS B1156 PHE 0.026 0.001 PHE A 589 TYR 0.021 0.001 TYR A 167 ARG 0.003 0.000 ARG H 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 196 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5854 (m-80) cc_final: 0.5636 (m-80) REVERT: A 174 MET cc_start: 0.1272 (mtt) cc_final: 0.0991 (mtt) REVERT: C 320 SER cc_start: 0.8445 (m) cc_final: 0.8170 (p) REVERT: C 487 LEU cc_start: 0.7178 (mm) cc_final: 0.6195 (tp) REVERT: C 913 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: H 17 SER cc_start: 0.5590 (OUTLIER) cc_final: 0.4909 (t) REVERT: H 78 LEU cc_start: 0.6489 (tp) cc_final: 0.5843 (tt) REVERT: H 83 ASN cc_start: 0.7918 (p0) cc_final: 0.7526 (t0) REVERT: D 71 PHE cc_start: 0.7486 (t80) cc_final: 0.7045 (t80) REVERT: D 86 TYR cc_start: 0.7201 (m-80) cc_final: 0.6869 (m-10) REVERT: D 87 TYR cc_start: 0.6257 (m-80) cc_final: 0.5762 (m-10) outliers start: 65 outliers final: 42 residues processed: 247 average time/residue: 0.3461 time to fit residues: 147.8901 Evaluate side-chains 230 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 154 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 213 optimal weight: 0.0060 chunk 229 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 264 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 950 ASN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28984 Z= 0.161 Angle : 0.562 9.795 39438 Z= 0.282 Chirality : 0.044 0.347 4587 Planarity : 0.004 0.054 5036 Dihedral : 5.317 59.291 4837 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.25 % Favored : 93.64 % Rotamer: Outliers : 1.94 % Allowed : 15.91 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.14), residues: 3489 helix: 0.93 (0.20), residues: 745 sheet: -0.40 (0.19), residues: 779 loop : -1.69 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 36 HIS 0.007 0.000 HIS B1156 PHE 0.025 0.001 PHE A 589 TYR 0.022 0.001 TYR C 468 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 195 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5866 (m-80) cc_final: 0.5622 (m-80) REVERT: A 174 MET cc_start: 0.1266 (mtt) cc_final: 0.0977 (mtt) REVERT: B 149 TRP cc_start: 0.5549 (t-100) cc_final: 0.5340 (t-100) REVERT: C 320 SER cc_start: 0.8577 (m) cc_final: 0.8260 (p) REVERT: C 487 LEU cc_start: 0.7161 (mm) cc_final: 0.6176 (tp) REVERT: H 17 SER cc_start: 0.5593 (OUTLIER) cc_final: 0.4901 (t) REVERT: H 83 ASN cc_start: 0.7911 (p0) cc_final: 0.7506 (t0) REVERT: D 71 PHE cc_start: 0.7482 (t80) cc_final: 0.7018 (t80) REVERT: D 86 TYR cc_start: 0.7153 (m-80) cc_final: 0.6822 (m-10) REVERT: D 87 TYR cc_start: 0.6270 (m-80) cc_final: 0.5759 (m-10) outliers start: 60 outliers final: 45 residues processed: 243 average time/residue: 0.3302 time to fit residues: 139.0951 Evaluate side-chains 232 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 186 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 936 THR Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 0.2980 chunk 294 optimal weight: 0.4980 chunk 313 optimal weight: 3.9990 chunk 188 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 chunk 296 optimal weight: 4.9990 chunk 312 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 314 ASN ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 185 ASN C 908 GLN C 950 ASN C1000 GLN ** C1154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28984 Z= 0.158 Angle : 0.561 9.611 39438 Z= 0.281 Chirality : 0.044 0.346 4587 Planarity : 0.004 0.053 5036 Dihedral : 5.178 57.456 4837 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.93 % Favored : 93.95 % Rotamer: Outliers : 1.88 % Allowed : 16.27 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3489 helix: 0.99 (0.19), residues: 746 sheet: -0.29 (0.19), residues: 762 loop : -1.66 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 36 HIS 0.007 0.000 HIS B1156 PHE 0.025 0.001 PHE A 589 TYR 0.020 0.001 TYR C 468 ARG 0.003 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6978 Ramachandran restraints generated. 3489 Oldfield, 0 Emsley, 3489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 197 time to evaluate : 3.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5920 (m-80) cc_final: 0.5660 (m-80) REVERT: A 167 TYR cc_start: 0.7094 (t80) cc_final: 0.6840 (t80) REVERT: A 174 MET cc_start: 0.1241 (mtt) cc_final: 0.0948 (mtt) REVERT: A 915 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: B 149 TRP cc_start: 0.5694 (t-100) cc_final: 0.5346 (t-100) REVERT: B 174 MET cc_start: 0.4400 (mmt) cc_final: 0.2537 (mtt) REVERT: C 320 SER cc_start: 0.8558 (m) cc_final: 0.8224 (p) REVERT: C 487 LEU cc_start: 0.7166 (mm) cc_final: 0.6172 (tp) REVERT: H 17 SER cc_start: 0.5561 (OUTLIER) cc_final: 0.4879 (t) REVERT: H 33 TYR cc_start: 0.4390 (m-10) cc_final: 0.4132 (m-10) REVERT: H 83 ASN cc_start: 0.7901 (p0) cc_final: 0.7496 (t0) REVERT: H 98 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4859 (pp20) REVERT: D 71 PHE cc_start: 0.7471 (t80) cc_final: 0.7000 (t80) REVERT: D 86 TYR cc_start: 0.7134 (m-80) cc_final: 0.6805 (m-10) REVERT: D 87 TYR cc_start: 0.6294 (m-80) cc_final: 0.5766 (m-10) outliers start: 58 outliers final: 48 residues processed: 239 average time/residue: 0.3360 time to fit residues: 137.7577 Evaluate side-chains 235 residues out of total 3095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 908 VAL Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1106 PHE Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 978 PHE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 382 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 622 ASP Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 868 TYR Chi-restraints excluded: chain C residue 906 VAL Chi-restraints excluded: chain C residue 913 GLU Chi-restraints excluded: chain C residue 1035 VAL Chi-restraints excluded: chain C residue 1114 ASN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 52.3847 > 50: distance: 28 - 30: 11.981 distance: 30 - 31: 9.267 distance: 31 - 32: 16.626 distance: 31 - 34: 8.159 distance: 32 - 33: 12.417 distance: 32 - 38: 10.624 distance: 34 - 35: 21.713 distance: 34 - 36: 20.903 distance: 35 - 37: 12.463 distance: 38 - 39: 7.631 distance: 39 - 40: 8.719 distance: 39 - 42: 10.259 distance: 40 - 41: 8.228 distance: 40 - 50: 16.677 distance: 42 - 43: 5.694 distance: 43 - 44: 4.447 distance: 43 - 45: 9.968 distance: 44 - 46: 7.371 distance: 45 - 47: 6.067 distance: 46 - 48: 9.345 distance: 47 - 48: 9.949 distance: 48 - 49: 9.314 distance: 50 - 51: 19.822 distance: 51 - 52: 18.958 distance: 51 - 54: 7.593 distance: 52 - 53: 20.325 distance: 52 - 59: 9.533 distance: 54 - 55: 18.680 distance: 55 - 56: 18.351 distance: 56 - 57: 12.535 distance: 56 - 58: 6.128 distance: 59 - 60: 14.399 distance: 60 - 61: 13.975 distance: 60 - 63: 18.534 distance: 61 - 62: 21.199 distance: 61 - 66: 17.563 distance: 63 - 64: 19.567 distance: 63 - 65: 10.386 distance: 66 - 67: 12.125 distance: 67 - 68: 7.311 distance: 67 - 70: 10.844 distance: 68 - 69: 6.868 distance: 68 - 72: 8.444 distance: 70 - 71: 4.457 distance: 72 - 73: 6.966 distance: 73 - 74: 9.340 distance: 73 - 76: 11.470 distance: 74 - 75: 11.053 distance: 74 - 80: 6.499 distance: 76 - 77: 9.697 distance: 77 - 78: 3.165 distance: 77 - 79: 6.965 distance: 80 - 81: 3.565 distance: 80 - 149: 7.281 distance: 81 - 82: 6.479 distance: 82 - 83: 7.786 distance: 82 - 91: 3.895 distance: 83 - 146: 18.974 distance: 84 - 85: 4.068 distance: 85 - 86: 5.523 distance: 85 - 87: 5.396 distance: 86 - 88: 3.660 distance: 88 - 90: 5.583 distance: 89 - 90: 7.373 distance: 92 - 93: 5.799 distance: 93 - 94: 3.605 distance: 93 - 102: 8.196 distance: 95 - 96: 5.617 distance: 97 - 98: 5.293 distance: 98 - 99: 6.753 distance: 99 - 100: 7.425 distance: 99 - 101: 12.800 distance: 102 - 103: 7.161 distance: 103 - 104: 8.906 distance: 103 - 106: 11.241 distance: 104 - 105: 25.650 distance: 104 - 109: 8.685 distance: 106 - 107: 6.052 distance: 106 - 108: 11.353 distance: 109 - 110: 5.777 distance: 110 - 113: 14.946 distance: 111 - 112: 8.684 distance: 113 - 114: 14.567 distance: 114 - 115: 15.759 distance: 115 - 116: 7.431 distance: 115 - 117: 9.263