Starting phenix.real_space_refine on Fri Aug 9 04:36:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u3k_41865/08_2024/8u3k_41865.cif" } resolution = 2.5 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= 0.001 sd= 0.011 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: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 15723 2.51 5 N 4282 2.21 5 O 4869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A ARG 119": "NH1" <-> "NH2" Residue "A ASP 152": "OD1" <-> "OD2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A ARG 176": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 352": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 360": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 511": "NH1" <-> "NH2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ASP 549": "OD1" <-> "OD2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 604": "NH1" <-> "NH2" Residue "A ASP 605": "OD1" <-> "OD2" Residue "A PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A TYR 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A ARG 768": "NH1" <-> "NH2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 828": "NH1" <-> "NH2" Residue "A ARG 830": "NH1" <-> "NH2" Residue "A ARG 846": "NH1" <-> "NH2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 858": "NH1" <-> "NH2" Residue "A ARG 863": "NH1" <-> "NH2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 914": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A ARG 936": "NH1" <-> "NH2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A ARG 959": "NH1" <-> "NH2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 968": "OE1" <-> "OE2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ARG 972": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "A PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1001": "NH1" <-> "NH2" Residue "A GLU 1011": "OE1" <-> "OE2" Residue "A TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1025": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A ARG 1083": "NH1" <-> "NH2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1145": "NH1" <-> "NH2" Residue "A TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1170": "OD1" <-> "OD2" Residue "A ASP 1174": "OD1" <-> "OD2" Residue "A ARG 1177": "NH1" <-> "NH2" Residue "A GLU 1182": "OE1" <-> "OE2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 202": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E ASP 330": "OD1" <-> "OD2" Residue "E ARG 341": "NH1" <-> "NH2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 367": "NH1" <-> "NH2" Residue "E ARG 382": "NH1" <-> "NH2" Residue "E ARG 386": "NH1" <-> "NH2" Residue "E ARG 392": "NH1" <-> "NH2" Residue "E ARG 411": "NH1" <-> "NH2" Residue "E TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 422": "OE1" <-> "OE2" Residue "E ARG 423": "NH1" <-> "NH2" Residue "E ARG 431": "NH1" <-> "NH2" Residue "E ARG 440": "NH1" <-> "NH2" Residue "E GLU 464": "OE1" <-> "OE2" Residue "E ARG 478": "NH1" <-> "NH2" Residue "E ARG 486": "NH1" <-> "NH2" Residue "E PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 518": "NH1" <-> "NH2" Residue "E ARG 520": "NH1" <-> "NH2" Residue "E ARG 526": "NH1" <-> "NH2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ARG 587": "NH1" <-> "NH2" Residue "E ARG 598": "NH1" <-> "NH2" Residue "E PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "E TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 662": "NH1" <-> "NH2" Residue "E ARG 664": "NH1" <-> "NH2" Residue "E ARG 677": "NH1" <-> "NH2" Residue "E ARG 684": "NH1" <-> "NH2" Residue "E ARG 686": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 119": "NH1" <-> "NH2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F ARG 176": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F ASP 201": "OD1" <-> "OD2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "F ARG 212": "NH1" <-> "NH2" Residue "F ARG 233": "NH1" <-> "NH2" Residue "F ARG 255": "NH1" <-> "NH2" Residue "F ARG 257": "NH1" <-> "NH2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 298": "NH1" <-> "NH2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 305": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F ARG 328": "NH1" <-> "NH2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F ARG 352": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 360": "NH1" <-> "NH2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 380": "NH1" <-> "NH2" Residue "F ARG 381": "NH1" <-> "NH2" Residue "F ARG 404": "NH1" <-> "NH2" Residue "F ARG 421": "NH1" <-> "NH2" Residue "F GLU 463": "OE1" <-> "OE2" Residue "F PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 511": "NH1" <-> "NH2" Residue "F ARG 547": "NH1" <-> "NH2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F ARG 573": "NH1" <-> "NH2" Residue "F ARG 578": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 587": "NH1" <-> "NH2" Residue "F ARG 604": "NH1" <-> "NH2" Residue "F ASP 605": "OD1" <-> "OD2" Residue "F PHE 607": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 641": "NH1" <-> "NH2" Residue "F ARG 661": "NH1" <-> "NH2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F ARG 675": "NH1" <-> "NH2" Residue "F ASP 706": "OD1" <-> "OD2" Residue "F ARG 709": "NH1" <-> "NH2" Residue "F PHE 730": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 768": "NH1" <-> "NH2" Residue "F ARG 820": "NH1" <-> "NH2" Residue "F ARG 828": "NH1" <-> "NH2" Residue "F ARG 830": "NH1" <-> "NH2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ARG 855": "NH1" <-> "NH2" Residue "F ARG 858": "NH1" <-> "NH2" Residue "F ARG 863": "NH1" <-> "NH2" Residue "F ARG 883": "NH1" <-> "NH2" Residue "F ARG 910": "NH1" <-> "NH2" Residue "F ARG 913": "NH1" <-> "NH2" Residue "F ARG 914": "NH1" <-> "NH2" Residue "F ARG 921": "NH1" <-> "NH2" Residue "F ARG 936": "NH1" <-> "NH2" Residue "F ARG 954": "NH1" <-> "NH2" Residue "F ARG 959": "NH1" <-> "NH2" Residue "F ARG 969": "NH1" <-> "NH2" Residue "F ARG 972": "NH1" <-> "NH2" Residue "F TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 984": "NH1" <-> "NH2" Residue "F PHE 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1001": "NH1" <-> "NH2" Residue "F GLU 1011": "OE1" <-> "OE2" Residue "F ARG 1025": "NH1" <-> "NH2" Residue "F ARG 1030": "NH1" <-> "NH2" Residue "F TYR 1081": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1083": "NH1" <-> "NH2" Residue "F ARG 1087": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F ASP 1170": "OD1" <-> "OD2" Residue "F ARG 1177": "NH1" <-> "NH2" Residue "F GLU 1182": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24990 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9279 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1116} Chain breaks: 4 Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 582 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 313 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "E" Number of atoms: 5453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5453 Classifications: {'peptide': 669} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 634} Chain breaks: 2 Chain: "F" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 9142 Classifications: {'peptide': 1133} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 1099} Chain breaks: 6 Chain: "G" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.53, per 1000 atoms: 0.58 Number of scatterers: 24990 At special positions: 0 Unit cell: (139.144, 153.309, 159.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 55 15.00 Mg 1 11.99 O 4869 8.00 N 4282 7.00 C 15723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.89 Conformation dependent library (CDL) restraints added in 4.5 seconds 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 31 sheets defined 51.1% alpha, 13.7% beta 10 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 8.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 54 through 77 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.829A pdb=" N CYS A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 removed outlier: 3.732A pdb=" N ALA A 161 " --> pdb=" O ASN A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 161' Processing helix chain 'A' and resid 162 through 178 removed outlier: 4.220A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 removed outlier: 4.011A pdb=" N GLY A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.142A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.230A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.516A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.566A pdb=" N ASP A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.687A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 400 through 428 removed outlier: 4.015A pdb=" N ARG A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 removed outlier: 4.390A pdb=" N GLN A 449 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 472 Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 621 through 629 Processing helix chain 'A' and resid 636 through 656 removed outlier: 3.560A pdb=" N LYS A 646 " --> pdb=" O SER A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 removed outlier: 3.709A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.541A pdb=" N SER A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.544A pdb=" N GLU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 747 through 752' Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.288A pdb=" N ASN A 793 " --> pdb=" O HIS A 790 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 794 " --> pdb=" O THR A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 808 removed outlier: 4.166A pdb=" N ILE A 801 " --> pdb=" O GLN A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 824 Processing helix chain 'A' and resid 827 through 837 removed outlier: 3.899A pdb=" N GLN A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 856 removed outlier: 3.940A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 879 Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.314A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 901 Processing helix chain 'A' and resid 909 through 938 removed outlier: 3.912A pdb=" N ARG A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 931 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.885A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1013 removed outlier: 3.629A pdb=" N CYS A1013 " --> pdb=" O GLU A1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1010 through 1013' Processing helix chain 'A' and resid 1014 through 1021 removed outlier: 3.875A pdb=" N ASN A1021 " --> pdb=" O THR A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 removed outlier: 3.763A pdb=" N TRP A1027 " --> pdb=" O TYR A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1068 removed outlier: 3.951A pdb=" N ALA A1068 " --> pdb=" O ALA A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1127 removed outlier: 3.716A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'E' and resid 45 through 50 removed outlier: 4.323A pdb=" N LYS E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 removed outlier: 4.263A pdb=" N GLY E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 184 through 187 Processing helix chain 'E' and resid 242 through 247 Processing helix chain 'E' and resid 249 through 266 removed outlier: 3.775A pdb=" N LYS E 262 " --> pdb=" O MET E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 297 Processing helix chain 'E' and resid 298 through 301 Processing helix chain 'E' and resid 317 through 329 removed outlier: 3.720A pdb=" N THR E 321 " --> pdb=" O ASP E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 391 through 411 removed outlier: 3.736A pdb=" N VAL E 395 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 473 removed outlier: 3.811A pdb=" N ASP E 468 " --> pdb=" O GLU E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 476 No H-bonds generated for 'chain 'E' and resid 474 through 476' Processing helix chain 'E' and resid 477 through 482 Processing helix chain 'E' and resid 511 through 527 Processing helix chain 'E' and resid 531 through 542 removed outlier: 3.719A pdb=" N LEU E 535 " --> pdb=" O PRO E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 558 Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.616A pdb=" N SER E 570 " --> pdb=" O ASP E 567 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR E 571 " --> pdb=" O GLU E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 649 through 657 Processing helix chain 'E' and resid 670 through 687 removed outlier: 3.917A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS E 675 " --> pdb=" O TYR E 671 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N PHE E 685 " --> pdb=" O GLU E 681 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG E 686 " --> pdb=" O MET E 682 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER E 687 " --> pdb=" O GLN E 683 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 20 through 38 removed outlier: 3.676A pdb=" N ILE F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 77 Processing helix chain 'F' and resid 78 through 81 removed outlier: 3.550A pdb=" N GLY F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 78 through 81' Processing helix chain 'F' and resid 94 through 112 Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.770A pdb=" N CYS F 145 " --> pdb=" O GLN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 157 Processing helix chain 'F' and resid 158 through 161 removed outlier: 3.910A pdb=" N ALA F 161 " --> pdb=" O ASN F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 158 through 161' Processing helix chain 'F' and resid 162 through 177 Processing helix chain 'F' and resid 181 through 209 Processing helix chain 'F' and resid 216 through 227 Processing helix chain 'F' and resid 228 through 234 removed outlier: 4.071A pdb=" N ILE F 232 " --> pdb=" O PRO F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 259 through 264 removed outlier: 4.030A pdb=" N LEU F 264 " --> pdb=" O LEU F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.572A pdb=" N LYS F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 304 Processing helix chain 'F' and resid 312 through 316 removed outlier: 3.553A pdb=" N ASP F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 337 Proline residue: F 324 - end of helix Processing helix chain 'F' and resid 401 through 428 Processing helix chain 'F' and resid 445 through 459 removed outlier: 4.294A pdb=" N GLN F 449 " --> pdb=" O GLU F 445 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU F 450 " --> pdb=" O GLY F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'F' and resid 464 through 472 Processing helix chain 'F' and resid 493 through 497 removed outlier: 3.530A pdb=" N HIS F 496 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 535 Processing helix chain 'F' and resid 556 through 565 Processing helix chain 'F' and resid 572 through 587 Processing helix chain 'F' and resid 604 through 616 Processing helix chain 'F' and resid 621 through 629 Processing helix chain 'F' and resid 636 through 656 removed outlier: 4.005A pdb=" N LYS F 646 " --> pdb=" O SER F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 675 through 694 removed outlier: 3.508A pdb=" N PHE F 681 " --> pdb=" O ASN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 711 Processing helix chain 'F' and resid 713 through 723 removed outlier: 3.505A pdb=" N SER F 717 " --> pdb=" O TYR F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.952A pdb=" N GLY F 752 " --> pdb=" O LEU F 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 793 removed outlier: 4.188A pdb=" N ASN F 793 " --> pdb=" O HIS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 807 removed outlier: 3.556A pdb=" N GLN F 800 " --> pdb=" O CYS F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 811 through 824 Processing helix chain 'F' and resid 827 through 836 Processing helix chain 'F' and resid 838 through 856 removed outlier: 4.135A pdb=" N GLN F 842 " --> pdb=" O THR F 838 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 856 " --> pdb=" O ALA F 852 " (cutoff:3.500A) Processing helix chain 'F' and resid 873 through 880 removed outlier: 4.494A pdb=" N ILE F 877 " --> pdb=" O GLY F 873 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU F 880 " --> pdb=" O GLU F 876 " (cutoff:3.500A) Processing helix chain 'F' and resid 884 through 888 removed outlier: 4.306A pdb=" N LEU F 887 " --> pdb=" O ASP F 884 " (cutoff:3.500A) Processing helix chain 'F' and resid 889 through 901 Processing helix chain 'F' and resid 909 through 939 removed outlier: 3.724A pdb=" N ARG F 913 " --> pdb=" O ASP F 909 " (cutoff:3.500A) Processing helix chain 'F' and resid 943 through 960 Processing helix chain 'F' and resid 970 through 972 No H-bonds generated for 'chain 'F' and resid 970 through 972' Processing helix chain 'F' and resid 1010 through 1013 removed outlier: 3.640A pdb=" N CYS F1013 " --> pdb=" O GLU F1010 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1010 through 1013' Processing helix chain 'F' and resid 1014 through 1020 Processing helix chain 'F' and resid 1023 through 1032 removed outlier: 3.689A pdb=" N TRP F1027 " --> pdb=" O TYR F1023 " (cutoff:3.500A) Processing helix chain 'F' and resid 1045 through 1052 Processing helix chain 'F' and resid 1052 through 1068 removed outlier: 3.660A pdb=" N ALA F1068 " --> pdb=" O ALA F1064 " (cutoff:3.500A) Processing helix chain 'F' and resid 1113 through 1127 removed outlier: 3.701A pdb=" N GLU F1125 " --> pdb=" O LEU F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.344A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 345 removed outlier: 6.423A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLU A 345 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 382 " --> pdb=" O ASP A 377 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP A 388 " --> pdb=" O LYS A 371 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 371 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.075A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AA8, first strand: chain 'A' and resid 744 through 745 Processing sheet with id=AA9, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AB1, first strand: chain 'A' and resid 962 through 963 removed outlier: 3.681A pdb=" N ASN A1042 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 983 through 985 Processing sheet with id=AB3, first strand: chain 'A' and resid 1071 through 1074 removed outlier: 3.535A pdb=" N ASN A1086 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.596A pdb=" N GLY A1138 " --> pdb=" O ILE A1168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 269 through 275 removed outlier: 6.675A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.642A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 19.976A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 30.626A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 34.208A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU E 638 " --> pdb=" O THR E 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 506 " --> pdb=" O SER E 636 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N SER E 636 " --> pdb=" O ILE E 506 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N HIS E 637 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA E 622 " --> pdb=" O HIS E 637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 269 through 275 removed outlier: 6.675A pdb=" N SER E 270 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE E 21 " --> pdb=" O SER E 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS E 272 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU E 17 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 14 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLN E 507 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 9.979A pdb=" N ILE E 18 " --> pdb=" O GLY E 505 " (cutoff:3.500A) removed outlier: 13.642A pdb=" N GLY E 505 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 19.976A pdb=" N GLN E 20 " --> pdb=" O ASP E 503 " (cutoff:3.500A) removed outlier: 23.560A pdb=" N ASP E 503 " --> pdb=" O GLN E 20 " (cutoff:3.500A) removed outlier: 30.626A pdb=" N SER E 22 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 34.208A pdb=" N PHE E 501 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 66 through 69 removed outlier: 3.677A pdb=" N CYS E 66 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE E 34 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 136 through 144 removed outlier: 6.384A pdb=" N TYR E 137 " --> pdb=" O ILE E 159 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE E 159 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU E 139 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL E 157 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR E 152 " --> pdb=" O PRO E 182 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 236 through 237 Processing sheet with id=AC1, first strand: chain 'E' and resid 334 through 336 removed outlier: 6.618A pdb=" N LEU E 305 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA E 336 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE E 307 " --> pdb=" O ALA E 336 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 43 through 47 removed outlier: 6.110A pdb=" N ALA F 43 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY F 541 " --> pdb=" O ALA F 43 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU F 45 " --> pdb=" O GLY F 541 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR F 89 " --> pdb=" O ILE F 270 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP F 272 " --> pdb=" O TYR F 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 91 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU F 88 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU F 242 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N TYR F 90 " --> pdb=" O LEU F 242 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AC4, first strand: chain 'F' and resid 251 through 252 Processing sheet with id=AC5, first strand: chain 'F' and resid 291 through 292 Processing sheet with id=AC6, first strand: chain 'F' and resid 342 through 345 removed outlier: 6.766A pdb=" N ASN F 343 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N SER F 387 " --> pdb=" O ASN F 343 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N GLU F 345 " --> pdb=" O SER F 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP F 388 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS F 371 " --> pdb=" O ASP F 388 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 595 through 601 removed outlier: 6.477A pdb=" N VAL F 595 " --> pdb=" O ILE F 866 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU F 868 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR F 597 " --> pdb=" O LEU F 868 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL F 870 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS F 599 " --> pdb=" O VAL F 870 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE F 774 " --> pdb=" O PHE F 869 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP F 871 " --> pdb=" O ILE F 774 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU F 776 " --> pdb=" O ASP F 871 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS F 698 " --> pdb=" O VAL F 728 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE F 730 " --> pdb=" O LYS F 698 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N PHE F 700 " --> pdb=" O PHE F 730 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N THR F 732 " --> pdb=" O PHE F 700 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 744 through 745 Processing sheet with id=AC9, first strand: chain 'F' and resid 755 through 757 Processing sheet with id=AD1, first strand: chain 'F' and resid 962 through 963 removed outlier: 3.692A pdb=" N ASN F1042 " --> pdb=" O VAL F 963 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 983 through 985 Processing sheet with id=AD3, first strand: chain 'F' and resid 1071 through 1074 removed outlier: 6.670A pdb=" N TRP F1098 " --> pdb=" O ILE F1132 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL F1134 " --> pdb=" O TRP F1098 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ASP F1100 " --> pdb=" O VAL F1134 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 1137 through 1138 1175 hydrogen bonds defined for protein. 3327 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 10.13 Time building geometry restraints manager: 10.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7273 1.33 - 1.46: 5911 1.46 - 1.58: 12229 1.58 - 1.71: 104 1.71 - 1.83: 93 Bond restraints: 25610 Sorted by residual: bond pdb=" CA ASN A 566 " pdb=" C ASN A 566 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.48e-02 4.57e+03 8.93e+00 bond pdb=" CA LYS F 287 " pdb=" C LYS F 287 " ideal model delta sigma weight residual 1.523 1.474 0.049 1.80e-02 3.09e+03 7.35e+00 bond pdb=" CG LEU A 782 " pdb=" CD1 LEU A 782 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.38e+00 bond pdb=" C PRO A 353 " pdb=" N VAL A 354 " ideal model delta sigma weight residual 1.331 1.299 0.031 1.27e-02 6.20e+03 6.14e+00 bond pdb=" CG LEU A 203 " pdb=" CD1 LEU A 203 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.79e+00 ... (remaining 25605 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.58: 489 104.58 - 112.14: 12554 112.14 - 119.71: 9184 119.71 - 127.28: 12329 127.28 - 134.85: 295 Bond angle restraints: 34851 Sorted by residual: angle pdb=" N GLU E 132 " pdb=" CA GLU E 132 " pdb=" C GLU E 132 " ideal model delta sigma weight residual 110.61 103.31 7.30 1.25e+00 6.40e-01 3.41e+01 angle pdb=" CA ILE F1119 " pdb=" CB ILE F1119 " pdb=" CG1 ILE F1119 " ideal model delta sigma weight residual 110.40 120.05 -9.65 1.70e+00 3.46e-01 3.22e+01 angle pdb=" CB LYS F 111 " pdb=" CG LYS F 111 " pdb=" CD LYS F 111 " ideal model delta sigma weight residual 111.30 123.67 -12.37 2.30e+00 1.89e-01 2.89e+01 angle pdb=" CB MET A 824 " pdb=" CG MET A 824 " pdb=" SD MET A 824 " ideal model delta sigma weight residual 112.70 127.55 -14.85 3.00e+00 1.11e-01 2.45e+01 angle pdb=" CA LYS F 944 " pdb=" CB LYS F 944 " pdb=" CG LYS F 944 " ideal model delta sigma weight residual 114.10 123.68 -9.58 2.00e+00 2.50e-01 2.29e+01 ... (remaining 34846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 14621 34.87 - 69.74: 635 69.74 - 104.61: 33 104.61 - 139.48: 0 139.48 - 174.35: 1 Dihedral angle restraints: 15290 sinusoidal: 6614 harmonic: 8676 Sorted by residual: dihedral pdb=" CA PHE F 999 " pdb=" C PHE F 999 " pdb=" N ASP F1000 " pdb=" CA ASP F1000 " ideal model delta harmonic sigma weight residual -180.00 -138.64 -41.36 0 5.00e+00 4.00e-02 6.84e+01 dihedral pdb=" CA PHE A 999 " pdb=" C PHE A 999 " pdb=" N ASP A1000 " pdb=" CA ASP A1000 " ideal model delta harmonic sigma weight residual -180.00 -140.48 -39.52 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CA TYR F 788 " pdb=" C TYR F 788 " pdb=" N SER F 789 " pdb=" CA SER F 789 " ideal model delta harmonic sigma weight residual -180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 15287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2454 0.041 - 0.082: 1002 0.082 - 0.123: 311 0.123 - 0.164: 63 0.164 - 0.205: 7 Chirality restraints: 3837 Sorted by residual: chirality pdb=" CA PRO E 380 " pdb=" N PRO E 380 " pdb=" C PRO E 380 " pdb=" CB PRO E 380 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE F 53 " pdb=" CA ILE F 53 " pdb=" CG1 ILE F 53 " pdb=" CG2 ILE F 53 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.48e-01 chirality pdb=" CA ASP E 330 " pdb=" N ASP E 330 " pdb=" C ASP E 330 " pdb=" CB ASP E 330 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.36e-01 ... (remaining 3834 not shown) Planarity restraints: 4321 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 379 " -0.065 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO E 380 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO E 380 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 380 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 131 " -0.035 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE E 131 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 131 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 131 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 131 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 131 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 131 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1076 " -0.050 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO A1077 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A1077 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A1077 " -0.041 5.00e-02 4.00e+02 ... (remaining 4318 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 222 2.59 - 3.17: 20893 3.17 - 3.75: 39604 3.75 - 4.32: 57429 4.32 - 4.90: 93102 Nonbonded interactions: 211250 Sorted by model distance: nonbonded pdb=" OP1 DA D 3 " pdb="MG MG D 101 " model vdw 2.016 2.170 nonbonded pdb=" OE1 GLN F 291 " pdb=" OH TYR F 413 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 983 " pdb=" O MET A1044 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR F 983 " pdb=" O MET F1044 " model vdw 2.214 3.040 nonbonded pdb=" O VAL E 28 " pdb=" N ARG E 30 " model vdw 2.221 3.120 ... (remaining 211245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 388 or resid 400 through 473 or resid 487 throug \ h 762 or resid 767 through 1190)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 6.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 73.850 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 25610 Z= 0.542 Angle : 0.828 16.551 34851 Z= 0.460 Chirality : 0.049 0.205 3837 Planarity : 0.005 0.095 4321 Dihedral : 17.428 174.352 9668 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Rotamer: Outliers : 1.60 % Allowed : 15.34 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 2922 helix: 0.75 (0.14), residues: 1323 sheet: -0.12 (0.25), residues: 419 loop : -0.55 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F1098 HIS 0.009 0.001 HIS A 458 PHE 0.055 0.003 PHE E 131 TYR 0.024 0.002 TYR A 848 ARG 0.028 0.001 ARG A1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 2.556 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8444 (mtmp) cc_final: 0.8168 (mtmm) REVERT: A 1067 THR cc_start: 0.9113 (t) cc_final: 0.8912 (m) REVERT: A 1145 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7551 (ttm-80) REVERT: E 328 HIS cc_start: 0.9100 (OUTLIER) cc_final: 0.8851 (m-70) REVERT: F 939 ASN cc_start: 0.8197 (m-40) cc_final: 0.7796 (p0) outliers start: 42 outliers final: 27 residues processed: 182 average time/residue: 1.3190 time to fit residues: 279.5404 Evaluate side-chains 162 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 403 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 602 ASN Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 1101 SER Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 459 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 607 PHE Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1137 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 233 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 836 HIS A1020 GLN E 328 HIS ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 683 GLN F 794 GLN F 940 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25610 Z= 0.201 Angle : 0.557 9.271 34851 Z= 0.301 Chirality : 0.041 0.153 3837 Planarity : 0.004 0.049 4321 Dihedral : 14.022 171.531 3848 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 2.94 % Allowed : 13.20 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.15), residues: 2922 helix: 1.63 (0.14), residues: 1356 sheet: -0.11 (0.25), residues: 426 loop : -0.42 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 643 HIS 0.007 0.001 HIS A 496 PHE 0.028 0.001 PHE E 131 TYR 0.017 0.001 TYR F 788 ARG 0.008 0.001 ARG A1083 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 144 time to evaluate : 3.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8482 (mtmp) cc_final: 0.8098 (mtmp) REVERT: A 214 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8378 (tm) REVERT: E 489 VAL cc_start: 0.8338 (OUTLIER) cc_final: 0.8065 (p) REVERT: F 177 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7941 (mmp80) REVERT: F 694 ASN cc_start: 0.8697 (t0) cc_final: 0.8494 (t0) REVERT: F 927 MET cc_start: 0.8644 (mtp) cc_final: 0.8440 (mtm) REVERT: F 939 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7717 (p0) REVERT: F 948 GLN cc_start: 0.9063 (tp40) cc_final: 0.8823 (mm-40) outliers start: 77 outliers final: 29 residues processed: 209 average time/residue: 1.3404 time to fit residues: 325.1950 Evaluate side-chains 160 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 128 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 271 optimal weight: 2.9990 chunk 292 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 268 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 291 GLN A 660 ASN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 HIS ** F 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 781 GLN F 951 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25610 Z= 0.368 Angle : 0.589 8.621 34851 Z= 0.315 Chirality : 0.043 0.160 3837 Planarity : 0.004 0.043 4321 Dihedral : 14.071 168.938 3829 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 2.79 % Allowed : 14.00 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.02 (0.16), residues: 2922 helix: 1.89 (0.14), residues: 1348 sheet: -0.13 (0.24), residues: 448 loop : -0.43 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 643 HIS 0.010 0.001 HIS A 496 PHE 0.031 0.002 PHE A 607 TYR 0.018 0.001 TYR F 788 ARG 0.008 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 139 time to evaluate : 2.997 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8523 (mtmp) cc_final: 0.8278 (mtmp) REVERT: A 214 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (tm) REVERT: A 1087 ARG cc_start: 0.8697 (mmm-85) cc_final: 0.8373 (mmm-85) REVERT: A 1145 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7565 (ttm-80) REVERT: E 428 MET cc_start: 0.8022 (ttm) cc_final: 0.7737 (ttp) REVERT: F 177 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7916 (mmp80) REVERT: F 927 MET cc_start: 0.8695 (mtp) cc_final: 0.8463 (mtm) REVERT: F 939 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7698 (p0) REVERT: F 948 GLN cc_start: 0.9063 (tp40) cc_final: 0.8803 (mm-40) REVERT: F 963 VAL cc_start: 0.8887 (OUTLIER) cc_final: 0.8657 (m) REVERT: F 1007 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: F 1186 TRP cc_start: 0.8136 (t60) cc_final: 0.7563 (t60) outliers start: 73 outliers final: 30 residues processed: 199 average time/residue: 1.3477 time to fit residues: 311.8556 Evaluate side-chains 164 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 796 CYS Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 322 LEU Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 513 THR Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1007 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 129 optimal weight: 0.4980 chunk 182 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 288 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 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 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 694 ASN F 951 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25610 Z= 0.197 Angle : 0.521 8.584 34851 Z= 0.280 Chirality : 0.040 0.159 3837 Planarity : 0.003 0.043 4321 Dihedral : 14.013 169.331 3828 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.50 % Favored : 97.36 % Rotamer: Outliers : 2.10 % Allowed : 14.88 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.29 (0.16), residues: 2922 helix: 2.23 (0.14), residues: 1332 sheet: -0.02 (0.25), residues: 432 loop : -0.40 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 643 HIS 0.005 0.001 HIS A 496 PHE 0.024 0.001 PHE A 607 TYR 0.018 0.001 TYR F 788 ARG 0.008 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8360 (tm) REVERT: A 939 ASN cc_start: 0.8120 (t0) cc_final: 0.7639 (p0) REVERT: A 1087 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.7815 (mmm-85) REVERT: E 382 ARG cc_start: 0.7824 (tpp80) cc_final: 0.7235 (ttp80) REVERT: E 428 MET cc_start: 0.7983 (ttm) cc_final: 0.7697 (ttp) REVERT: E 489 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8059 (p) REVERT: F 172 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9087 (mm) REVERT: F 177 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7889 (mmp80) REVERT: F 939 ASN cc_start: 0.7971 (m-40) cc_final: 0.7610 (p0) REVERT: F 963 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8560 (m) REVERT: F 1186 TRP cc_start: 0.8090 (t60) cc_final: 0.7553 (t60) outliers start: 55 outliers final: 20 residues processed: 196 average time/residue: 1.3857 time to fit residues: 315.1564 Evaluate side-chains 155 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 245 optimal weight: 0.0980 chunk 199 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 72 optimal weight: 0.0060 overall best weight: 2.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 719 HIS A 821 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 25610 Z= 0.433 Angle : 0.608 12.379 34851 Z= 0.321 Chirality : 0.045 0.166 3837 Planarity : 0.004 0.044 4321 Dihedral : 14.192 167.435 3821 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 2.44 % Allowed : 14.99 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.17 (0.16), residues: 2922 helix: 2.12 (0.14), residues: 1334 sheet: -0.07 (0.24), residues: 448 loop : -0.46 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1098 HIS 0.008 0.001 HIS A 496 PHE 0.032 0.002 PHE A 607 TYR 0.018 0.002 TYR F 788 ARG 0.006 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 134 time to evaluate : 2.852 Fit side-chains revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8537 (mtmp) cc_final: 0.8258 (mtmp) REVERT: A 214 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8466 (tm) REVERT: A 397 GLU cc_start: -0.3285 (OUTLIER) cc_final: -0.4995 (pm20) REVERT: A 939 ASN cc_start: 0.8143 (t0) cc_final: 0.7622 (p0) REVERT: F 172 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9140 (mm) REVERT: F 177 ARG cc_start: 0.8262 (mmt-90) cc_final: 0.7892 (mmp80) REVERT: F 939 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7744 (p0) REVERT: F 963 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8551 (m) REVERT: F 1007 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8165 (ttp) REVERT: F 1093 ILE cc_start: 0.6416 (OUTLIER) cc_final: 0.6188 (tt) REVERT: F 1186 TRP cc_start: 0.8133 (t60) cc_final: 0.7563 (t60) outliers start: 64 outliers final: 32 residues processed: 190 average time/residue: 1.3707 time to fit residues: 303.0760 Evaluate side-chains 170 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 234 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 201 ASP Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1007 MET Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 0.7980 chunk 259 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25610 Z= 0.219 Angle : 0.538 13.501 34851 Z= 0.286 Chirality : 0.040 0.161 3837 Planarity : 0.003 0.044 4321 Dihedral : 14.217 168.377 3821 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.46 % Favored : 97.40 % Rotamer: Outliers : 2.25 % Allowed : 15.64 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.38 (0.16), residues: 2922 helix: 2.31 (0.14), residues: 1334 sheet: 0.08 (0.25), residues: 431 loop : -0.40 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1098 HIS 0.005 0.001 HIS A 799 PHE 0.025 0.001 PHE A 607 TYR 0.017 0.001 TYR F 788 ARG 0.011 0.000 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 136 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8526 (mtmp) cc_final: 0.8235 (mtmp) REVERT: A 214 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8417 (tm) REVERT: A 397 GLU cc_start: -0.3368 (OUTLIER) cc_final: -0.5048 (pm20) REVERT: A 858 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7488 (mtp180) REVERT: A 939 ASN cc_start: 0.8136 (t0) cc_final: 0.7648 (p0) REVERT: A 1145 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7589 (ttm-80) REVERT: F 172 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9140 (mm) REVERT: F 177 ARG cc_start: 0.8254 (mmt-90) cc_final: 0.7857 (mmp80) REVERT: F 663 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7651 (ttt) REVERT: F 939 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7681 (p0) REVERT: F 963 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8527 (m) REVERT: F 1093 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6193 (tt) REVERT: F 1186 TRP cc_start: 0.8108 (t60) cc_final: 0.7519 (t60) outliers start: 59 outliers final: 30 residues processed: 186 average time/residue: 1.3971 time to fit residues: 302.8131 Evaluate side-chains 169 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 131 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 297 PHE Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 663 MET Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 945 SER Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1093 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 164 optimal weight: 0.2980 chunk 210 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 242 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 287 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25610 Z= 0.285 Angle : 0.559 13.890 34851 Z= 0.295 Chirality : 0.041 0.163 3837 Planarity : 0.004 0.044 4321 Dihedral : 14.272 167.739 3821 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.89 % Rotamer: Outliers : 2.17 % Allowed : 16.14 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.39 (0.16), residues: 2922 helix: 2.33 (0.14), residues: 1332 sheet: 0.05 (0.25), residues: 433 loop : -0.38 (0.18), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 643 HIS 0.006 0.001 HIS A 496 PHE 0.028 0.002 PHE A 607 TYR 0.017 0.001 TYR F 788 ARG 0.007 0.000 ARG A 969 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 133 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8527 (mtmp) cc_final: 0.8238 (mtmp) REVERT: A 214 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8443 (tm) REVERT: A 397 GLU cc_start: -0.3385 (OUTLIER) cc_final: -0.5078 (pm20) REVERT: A 858 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7444 (mtp180) REVERT: A 939 ASN cc_start: 0.8143 (t0) cc_final: 0.7639 (p0) REVERT: E 682 MET cc_start: 0.8503 (mtt) cc_final: 0.8293 (mtt) REVERT: F 172 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9143 (mm) REVERT: F 177 ARG cc_start: 0.8258 (mmt-90) cc_final: 0.7872 (mmp80) REVERT: F 201 ASP cc_start: 0.8375 (t0) cc_final: 0.8145 (t0) REVERT: F 205 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8853 (mttp) REVERT: F 939 ASN cc_start: 0.8023 (OUTLIER) cc_final: 0.7699 (p0) REVERT: F 963 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8502 (m) REVERT: F 1007 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8118 (ttp) REVERT: F 1186 TRP cc_start: 0.8124 (t60) cc_final: 0.7549 (t60) outliers start: 57 outliers final: 33 residues processed: 182 average time/residue: 1.3303 time to fit residues: 283.6702 Evaluate side-chains 172 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 787 ASP Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 691 LYS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 945 SER Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Chi-restraints excluded: chain F residue 1007 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 195 optimal weight: 0.3980 chunk 142 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25610 Z= 0.198 Angle : 0.546 14.258 34851 Z= 0.287 Chirality : 0.040 0.160 3837 Planarity : 0.003 0.044 4321 Dihedral : 14.219 168.277 3821 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 2.17 % Allowed : 16.25 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.16), residues: 2922 helix: 2.40 (0.14), residues: 1332 sheet: 0.12 (0.25), residues: 431 loop : -0.34 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A1098 HIS 0.005 0.001 HIS A 799 PHE 0.024 0.001 PHE A 607 TYR 0.016 0.001 TYR F 788 ARG 0.013 0.000 ARG A1145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 141 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8511 (mtmp) cc_final: 0.8280 (mtmp) REVERT: A 214 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8399 (tm) REVERT: A 397 GLU cc_start: -0.3307 (OUTLIER) cc_final: -0.4998 (pm20) REVERT: A 858 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7425 (mtp180) REVERT: A 939 ASN cc_start: 0.8161 (t0) cc_final: 0.7668 (p0) REVERT: F 177 ARG cc_start: 0.8245 (mmt-90) cc_final: 0.7844 (mmp80) REVERT: F 201 ASP cc_start: 0.8413 (t0) cc_final: 0.8164 (t0) REVERT: F 205 LYS cc_start: 0.9293 (ttmm) cc_final: 0.8843 (mttp) REVERT: F 939 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7648 (p0) REVERT: F 963 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8496 (m) REVERT: F 1186 TRP cc_start: 0.8118 (t60) cc_final: 0.7534 (t60) outliers start: 57 outliers final: 27 residues processed: 189 average time/residue: 1.3459 time to fit residues: 298.4735 Evaluate side-chains 166 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 2.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 323 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 945 SER Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 2.9990 chunk 275 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 241 optimal weight: 7.9990 chunk 253 optimal weight: 0.6980 chunk 266 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25610 Z= 0.284 Angle : 0.569 15.689 34851 Z= 0.298 Chirality : 0.041 0.163 3837 Planarity : 0.004 0.044 4321 Dihedral : 14.247 167.875 3821 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.15 % Favored : 96.71 % Rotamer: Outliers : 1.79 % Allowed : 16.94 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.45 (0.16), residues: 2922 helix: 2.39 (0.14), residues: 1328 sheet: 0.09 (0.25), residues: 433 loop : -0.37 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A1098 HIS 0.007 0.001 HIS E 409 PHE 0.028 0.002 PHE E 131 TYR 0.017 0.001 TYR F 788 ARG 0.010 0.000 ARG A1145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 136 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8548 (mtmp) cc_final: 0.8280 (mtmp) REVERT: A 214 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8436 (tm) REVERT: A 397 GLU cc_start: -0.3288 (OUTLIER) cc_final: -0.5010 (pm20) REVERT: A 858 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7408 (mtp180) REVERT: A 939 ASN cc_start: 0.8144 (t0) cc_final: 0.7676 (p0) REVERT: E 682 MET cc_start: 0.8501 (mtt) cc_final: 0.8276 (mtt) REVERT: F 177 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7851 (mmp80) REVERT: F 939 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7670 (p0) REVERT: F 963 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8477 (m) REVERT: F 1186 TRP cc_start: 0.8138 (t60) cc_final: 0.7577 (t60) outliers start: 47 outliers final: 25 residues processed: 177 average time/residue: 1.3212 time to fit residues: 273.8732 Evaluate side-chains 166 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 945 SER Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 236 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1020 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25610 Z= 0.345 Angle : 0.604 15.641 34851 Z= 0.316 Chirality : 0.043 0.164 3837 Planarity : 0.004 0.054 4321 Dihedral : 14.281 167.746 3819 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.89 % Rotamer: Outliers : 1.45 % Allowed : 17.44 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.39 (0.16), residues: 2922 helix: 2.34 (0.14), residues: 1328 sheet: 0.11 (0.25), residues: 431 loop : -0.40 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1098 HIS 0.008 0.001 HIS E 409 PHE 0.033 0.002 PHE E 131 TYR 0.017 0.001 TYR F 788 ARG 0.015 0.000 ARG A1145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5844 Ramachandran restraints generated. 2922 Oldfield, 0 Emsley, 2922 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 137 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 LYS cc_start: 0.8547 (mtmp) cc_final: 0.8262 (mtmp) REVERT: A 214 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8468 (tm) REVERT: A 397 GLU cc_start: -0.3016 (OUTLIER) cc_final: -0.4964 (pm20) REVERT: A 858 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: A 939 ASN cc_start: 0.8132 (t0) cc_final: 0.7698 (p0) REVERT: F 177 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7851 (mmp80) REVERT: F 939 ASN cc_start: 0.8046 (OUTLIER) cc_final: 0.7722 (p0) REVERT: F 963 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8485 (m) REVERT: F 1186 TRP cc_start: 0.8140 (t60) cc_final: 0.7570 (t60) outliers start: 38 outliers final: 28 residues processed: 170 average time/residue: 1.3644 time to fit residues: 270.7442 Evaluate side-chains 167 residues out of total 2621 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 489 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 763 TYR Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 999 PHE Chi-restraints excluded: chain A residue 1137 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 293 TYR Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 462 THR Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 387 SER Chi-restraints excluded: chain F residue 514 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 731 SER Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 870 VAL Chi-restraints excluded: chain F residue 939 ASN Chi-restraints excluded: chain F residue 945 SER Chi-restraints excluded: chain F residue 963 VAL Chi-restraints excluded: chain F residue 999 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 0.9990 chunk 251 optimal weight: 2.9990 chunk 72 optimal weight: 0.0070 chunk 217 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 236 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** F 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.082719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.058228 restraints weight = 70524.516| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.43 r_work: 0.3066 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25610 Z= 0.197 Angle : 0.554 15.409 34851 Z= 0.291 Chirality : 0.040 0.160 3837 Planarity : 0.004 0.046 4321 Dihedral : 14.203 169.076 3819 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.94 % Favored : 96.92 % Rotamer: Outliers : 1.49 % Allowed : 17.55 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1.49 (0.16), residues: 2922 helix: 2.42 (0.14), residues: 1340 sheet: 0.16 (0.25), residues: 430 loop : -0.39 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A1098 HIS 0.006 0.001 HIS E 409 PHE 0.030 0.001 PHE E 131 TYR 0.016 0.001 TYR F 788 ARG 0.012 0.000 ARG A1087 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8057.30 seconds wall clock time: 142 minutes 58.52 seconds (8578.52 seconds total)