Starting phenix.real_space_refine on Sat Jul 27 05:24:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yux_34114/07_2024/7yux_34114.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.037 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 126 5.16 5 C 23078 2.51 5 N 6427 2.21 5 O 6944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 453": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 662": "OD1" <-> "OD2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 656": "OD1" <-> "OD2" Residue "C TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 486": "OE1" <-> "OE2" Residue "E GLU 705": "OE1" <-> "OE2" Residue "D GLU 228": "OE1" <-> "OE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 434": "OD1" <-> "OD2" Residue "D PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F GLU 236": "OE1" <-> "OE2" Residue "F TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 241": "OD1" <-> "OD2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B ASP 453": "OD1" <-> "OD2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 635": "OE1" <-> "OE2" Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.82s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 36585 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.27, per 1000 atoms: 0.50 Number of scatterers: 36585 At special positions: 0 Unit cell: (174.66, 155.8, 179.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 P 10 15.00 O 6944 8.00 N 6427 7.00 C 23078 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: 13.41 Conformation dependent library (CDL) restraints added in 6.3 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 42 sheets defined 47.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 30 through 38 removed outlier: 4.197A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N MET A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.646A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.928A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.799A pdb=" N VAL A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 172 through 182 removed outlier: 4.180A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 237 Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.733A pdb=" N LEU A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.609A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.649A pdb=" N THR A 311 " --> pdb=" O ASP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.642A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG A 336 " --> pdb=" O TYR A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.713A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 423 through 427 removed outlier: 3.682A pdb=" N MET A 427 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.218A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 3.798A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.661A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.688A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.967A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.159A pdb=" N GLU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.745A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.675A pdb=" N VAL C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 138 removed outlier: 3.640A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.820A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 234 removed outlier: 3.686A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.895A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.836A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.945A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 434 through 442 removed outlier: 4.457A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.665A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.570A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 506 through 515 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.933A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 630 through 646 removed outlier: 3.743A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.930A pdb=" N ALA C 728 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 747 through 753 removed outlier: 3.707A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.552A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 39 removed outlier: 4.286A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 139 removed outlier: 3.719A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.795A pdb=" N LEU E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 150 " --> pdb=" O TYR E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 150' Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.738A pdb=" N LEU E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 234 Processing helix chain 'E' and resid 239 through 256 removed outlier: 4.291A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 272 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 308 through 319 removed outlier: 3.708A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 337 removed outlier: 4.336A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.177A pdb=" N ASP E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.808A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 648 through 652 removed outlier: 4.277A pdb=" N GLY E 652 " --> pdb=" O GLN E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.749A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS E 726 " --> pdb=" O LEU E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 761 through 767 removed outlier: 4.164A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 40 removed outlier: 4.201A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.633A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 184 through 234 Processing helix chain 'D' and resid 243 through 255 removed outlier: 3.705A pdb=" N GLU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 270 removed outlier: 3.586A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS D 265 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.026A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.633A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 386 through 391 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.582A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 473 through 477 Processing helix chain 'D' and resid 494 through 506 removed outlier: 3.599A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 515 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.657A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 586 through 590 removed outlier: 3.517A pdb=" N GLU D 589 " --> pdb=" O ASP D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.560A pdb=" N ALA D 646 " --> pdb=" O THR D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 742 through 746 removed outlier: 3.773A pdb=" N LEU D 746 " --> pdb=" O LEU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 Processing helix chain 'D' and resid 761 through 769 removed outlier: 3.835A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.562A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 139 removed outlier: 3.565A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 151 removed outlier: 3.934A pdb=" N LEU F 149 " --> pdb=" O ASP F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 169 Processing helix chain 'F' and resid 173 through 182 Processing helix chain 'F' and resid 184 through 235 removed outlier: 3.512A pdb=" N ARG F 188 " --> pdb=" O ASP F 184 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS F 235 " --> pdb=" O LYS F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.480A pdb=" N ALA F 248 " --> pdb=" O SER F 244 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 272 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 308 through 317 Processing helix chain 'F' and resid 324 through 338 removed outlier: 4.038A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 Processing helix chain 'F' and resid 403 through 412 Processing helix chain 'F' and resid 434 through 444 removed outlier: 4.456A pdb=" N ALA F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 483 removed outlier: 3.880A pdb=" N ASP F 483 " --> pdb=" O PRO F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 515 Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 541 through 560 Processing helix chain 'F' and resid 573 through 578 removed outlier: 4.048A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 647 Processing helix chain 'F' and resid 648 through 651 removed outlier: 3.603A pdb=" N TYR F 651 " --> pdb=" O THR F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 679 through 693 removed outlier: 3.527A pdb=" N MET F 683 " --> pdb=" O ALA F 679 " (cutoff:3.500A) Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.723A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 745 removed outlier: 4.407A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 Processing helix chain 'F' and resid 761 through 767 removed outlier: 3.618A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU F 767 " --> pdb=" O GLY F 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 118 through 137 Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.236A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.827A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.906A pdb=" N GLN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 241 removed outlier: 4.387A pdb=" N ASP B 241 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.808A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 319 through 324 removed outlier: 3.964A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP B 324 " --> pdb=" O GLY B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 339 removed outlier: 3.828A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 444 removed outlier: 3.936A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 removed outlier: 3.969A pdb=" N ASN B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.926A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 494 through 505 removed outlier: 3.686A pdb=" N GLN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 524 through 535 removed outlier: 4.106A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.916A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 739 through 745 removed outlier: 3.692A pdb=" N GLU B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 770 removed outlier: 3.849A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.656A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 10 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.656A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 10 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 93 " --> pdb=" O GLU A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 353 removed outlier: 3.706A pdb=" N THR A 470 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.346A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.748A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.539A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 732 through 736 removed outlier: 3.555A pdb=" N ILE A 733 " --> pdb=" O GLU A 755 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.747A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 73 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLU C 87 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 71 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ARG C 89 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA C 69 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG C 91 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 67 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN C 93 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TRP C 65 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 45 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 379 through 380 removed outlier: 7.388A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 353 " --> pdb=" O ALA C 471 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.624A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 596 through 603 removed outlier: 3.505A pdb=" N ALA C 601 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 617 through 618 removed outlier: 3.740A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 732 through 736 removed outlier: 7.468A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.666A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET E 85 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.666A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 419 " --> pdb=" O PHE E 466 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 520 through 522 Processing sheet with id=AB9, first strand: chain 'E' and resid 596 through 597 Processing sheet with id=AC1, first strand: chain 'E' and resid 600 through 601 removed outlier: 3.989A pdb=" N ALA E 601 " --> pdb=" O THR E 608 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 608 " --> pdb=" O ALA E 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 732 through 736 removed outlier: 7.166A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.793A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 21 through 25 removed outlier: 7.337A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 21 through 25 removed outlier: 7.337A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.923A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU D 353 " --> pdb=" O ALA D 471 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC8, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.595A pdb=" N GLY D 599 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.932A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.419A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.697A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.939A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N MET F 85 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 87 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLN F 68 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP F 65 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA F 48 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 379 through 380 removed outlier: 7.303A pdb=" N ILE F 379 " --> pdb=" O ASP F 422 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AD6, first strand: chain 'F' and resid 596 through 601 removed outlier: 6.584A pdb=" N SER F 624 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 735 through 736 removed outlier: 6.353A pdb=" N LEU F 735 " --> pdb=" O VAL F 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.578A pdb=" N PHE B 45 " --> pdb=" O PRO B 6 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AE1, first strand: chain 'B' and resid 65 through 67 Processing sheet with id=AE2, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AE3, first strand: chain 'B' and resid 451 through 452 removed outlier: 3.580A pdb=" N PHE B 451 " --> pdb=" O TYR B 460 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 597 through 601 removed outlier: 4.095A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 614 through 615 removed outlier: 3.690A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 732 through 736 removed outlier: 7.071A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1582 hydrogen bonds defined for protein. 4575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.35 Time building geometry restraints manager: 14.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12210 1.34 - 1.46: 4302 1.46 - 1.58: 20469 1.58 - 1.70: 16 1.70 - 1.81: 252 Bond restraints: 37249 Sorted by residual: bond pdb=" C ILE B 233 " pdb=" O ILE B 233 " ideal model delta sigma weight residual 1.236 1.341 -0.105 1.19e-02 7.06e+03 7.83e+01 bond pdb=" N ILE D 233 " pdb=" CA ILE D 233 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.07e-02 8.73e+03 1.21e+01 bond pdb=" N GLN B 234 " pdb=" CA GLN B 234 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.36e+00 bond pdb=" N LEU D 237 " pdb=" CA LEU D 237 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.01e+00 bond pdb=" N GLU F 240 " pdb=" CA GLU F 240 " ideal model delta sigma weight residual 1.455 1.492 -0.038 1.26e-02 6.30e+03 8.86e+00 ... (remaining 37244 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.97: 1122 105.97 - 113.58: 20975 113.58 - 121.20: 18221 121.20 - 128.82: 9953 128.82 - 136.43: 234 Bond angle restraints: 50505 Sorted by residual: angle pdb=" N VAL C 605 " pdb=" CA VAL C 605 " pdb=" C VAL C 605 " ideal model delta sigma weight residual 111.91 106.23 5.68 8.90e-01 1.26e+00 4.07e+01 angle pdb=" N ILE D 233 " pdb=" CA ILE D 233 " pdb=" C ILE D 233 " ideal model delta sigma weight residual 113.10 108.01 5.09 9.70e-01 1.06e+00 2.75e+01 angle pdb=" C LYS B 235 " pdb=" CA LYS B 235 " pdb=" CB LYS B 235 " ideal model delta sigma weight residual 110.06 117.47 -7.41 1.44e+00 4.82e-01 2.65e+01 angle pdb=" CA LEU B 243 " pdb=" C LEU B 243 " pdb=" O LEU B 243 " ideal model delta sigma weight residual 121.84 116.28 5.56 1.16e+00 7.43e-01 2.30e+01 angle pdb=" N GLU B 247 " pdb=" CA GLU B 247 " pdb=" C GLU B 247 " ideal model delta sigma weight residual 111.96 105.39 6.57 1.41e+00 5.03e-01 2.17e+01 ... (remaining 50500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 22653 35.28 - 70.57: 278 70.57 - 105.85: 39 105.85 - 141.13: 7 141.13 - 176.42: 4 Dihedral angle restraints: 22981 sinusoidal: 9595 harmonic: 13386 Sorted by residual: dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -131.72 -48.28 0 5.00e+00 4.00e-02 9.32e+01 dihedral pdb=" CA ASP F 51 " pdb=" C ASP F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta harmonic sigma weight residual -180.00 -134.73 -45.27 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -142.33 -37.67 0 5.00e+00 4.00e-02 5.68e+01 ... (remaining 22978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4730 0.058 - 0.116: 904 0.116 - 0.173: 97 0.173 - 0.231: 9 0.231 - 0.289: 4 Chirality restraints: 5744 Sorted by residual: chirality pdb=" CA ASP B 241 " pdb=" N ASP B 241 " pdb=" C ASP B 241 " pdb=" CB ASP B 241 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA LEU F 237 " pdb=" N LEU F 237 " pdb=" C LEU F 237 " pdb=" CB LEU F 237 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA LYS B 235 " pdb=" N LYS B 235 " pdb=" C LYS B 235 " pdb=" CB LYS B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 5741 not shown) Planarity restraints: 6557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " 0.028 2.00e-02 2.50e+03 5.55e-02 3.09e+01 pdb=" C ILE B 233 " -0.096 2.00e-02 2.50e+03 pdb=" O ILE B 233 " 0.034 2.00e-02 2.50e+03 pdb=" N GLN B 234 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 667 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO B 668 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO B 668 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 668 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.018 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B 602 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.003 2.00e-02 2.50e+03 ... (remaining 6554 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 452 2.64 - 3.20: 34235 3.20 - 3.77: 58156 3.77 - 4.33: 78455 4.33 - 4.90: 125675 Nonbonded interactions: 296973 Sorted by model distance: nonbonded pdb=" OG1 THR C 603 " pdb=" O GLY C 606 " model vdw 2.071 2.440 nonbonded pdb=" OE1 GLN C 277 " pdb=" OG1 THR C 284 " model vdw 2.112 2.440 nonbonded pdb=" OG1 THR E 603 " pdb=" O GLY E 606 " model vdw 2.128 2.440 nonbonded pdb=" OD1 ASP A 218 " pdb=" NH1 ARG D 198 " model vdw 2.129 2.520 nonbonded pdb=" OG1 THR F 603 " pdb=" O GLY F 606 " model vdw 2.141 2.440 ... (remaining 296968 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) selection = (chain 'D' and resid 2 through 774) selection = (chain 'E' and resid 2 through 774) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 1.380 Check model and map are aligned: 0.240 Set scattering table: 0.330 Process input model: 89.230 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 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 : 0.003 0.105 37249 Z= 0.211 Angle : 0.698 9.627 50505 Z= 0.383 Chirality : 0.045 0.289 5744 Planarity : 0.005 0.104 6557 Dihedral : 13.368 176.416 14365 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.36 % Favored : 93.56 % Rotamer: Outliers : 0.26 % Allowed : 0.41 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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: -1.09 (0.13), residues: 4626 helix: 0.59 (0.12), residues: 1937 sheet: -2.16 (0.21), residues: 547 loop : -1.54 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 602 HIS 0.005 0.001 HIS F 407 PHE 0.012 0.001 PHE A 657 TYR 0.028 0.001 TYR F 63 ARG 0.008 0.000 ARG D 198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 426 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6426 (tpt) cc_final: 0.5617 (mpp) REVERT: A 682 THR cc_start: 0.8254 (m) cc_final: 0.7980 (p) REVERT: C 425 ASP cc_start: 0.8830 (p0) cc_final: 0.8355 (p0) REVERT: C 473 THR cc_start: 0.8152 (m) cc_final: 0.7878 (p) REVERT: E 241 ASP cc_start: 0.2392 (OUTLIER) cc_final: 0.1345 (m-30) REVERT: E 243 LEU cc_start: 0.5995 (tp) cc_final: 0.5573 (mt) REVERT: E 512 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6368 (tpt90) REVERT: E 563 TRP cc_start: 0.5276 (p90) cc_final: 0.4328 (p90) REVERT: D 625 LEU cc_start: 0.7625 (mp) cc_final: 0.7275 (mp) REVERT: F 218 ASP cc_start: 0.7849 (m-30) cc_final: 0.7613 (p0) REVERT: F 427 MET cc_start: 0.3069 (mmp) cc_final: 0.2139 (mmp) REVERT: F 439 MET cc_start: 0.6887 (mtt) cc_final: 0.6662 (mtp) REVERT: F 496 MET cc_start: 0.7729 (tpt) cc_final: 0.7378 (tpt) REVERT: F 633 MET cc_start: 0.8264 (mpp) cc_final: 0.7708 (mpp) REVERT: B 171 TRP cc_start: 0.0010 (p90) cc_final: -0.0234 (p90) REVERT: B 245 ASP cc_start: 0.5926 (m-30) cc_final: 0.5712 (m-30) REVERT: B 386 ASP cc_start: 0.8497 (p0) cc_final: 0.7867 (p0) REVERT: B 476 THR cc_start: 0.8308 (t) cc_final: 0.7021 (m) outliers start: 10 outliers final: 4 residues processed: 435 average time/residue: 0.4362 time to fit residues: 319.3050 Evaluate side-chains 322 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 317 time to evaluate : 4.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 247 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 390 optimal weight: 50.0000 chunk 350 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 236 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 220 optimal weight: 0.3980 chunk 269 optimal weight: 9.9990 chunk 419 optimal weight: 9.9990 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 73 GLN A 220 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 HIS A 319 HIS C 83 GLN C 278 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 37249 Z= 0.382 Angle : 0.753 10.361 50505 Z= 0.377 Chirality : 0.047 0.238 5744 Planarity : 0.006 0.073 6557 Dihedral : 8.984 173.983 5172 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.19 % Favored : 91.74 % Rotamer: Outliers : 1.41 % Allowed : 9.12 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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: -1.51 (0.12), residues: 4626 helix: 0.21 (0.12), residues: 2023 sheet: -2.26 (0.21), residues: 554 loop : -1.85 (0.14), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.010 0.002 HIS C 407 PHE 0.026 0.002 PHE C 466 TYR 0.024 0.002 TYR A 493 ARG 0.009 0.001 ARG F 519 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 344 time to evaluate : 4.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6367 (tpt) cc_final: 0.5527 (mpp) REVERT: A 409 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: A 682 THR cc_start: 0.8540 (m) cc_final: 0.8246 (p) REVERT: A 698 MET cc_start: 0.2007 (mmt) cc_final: 0.1582 (mmt) REVERT: A 713 MET cc_start: 0.6512 (tmm) cc_final: 0.6283 (tmm) REVERT: C 160 MET cc_start: -0.1077 (mpp) cc_final: -0.1297 (mpp) REVERT: C 425 ASP cc_start: 0.8961 (p0) cc_final: 0.8587 (p0) REVERT: C 735 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7888 (mp) REVERT: E 563 TRP cc_start: 0.5472 (p90) cc_final: 0.4716 (p90) REVERT: E 620 SER cc_start: 0.7987 (m) cc_final: 0.7550 (t) REVERT: E 764 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7083 (mt-10) REVERT: D 401 MET cc_start: 0.6739 (tpp) cc_final: 0.6474 (tpp) REVERT: D 625 LEU cc_start: 0.7788 (mp) cc_final: 0.7546 (mp) REVERT: F 439 MET cc_start: 0.6866 (mtt) cc_final: 0.6635 (mtp) REVERT: F 633 MET cc_start: 0.8154 (mpp) cc_final: 0.7557 (mpp) REVERT: F 683 MET cc_start: 0.8224 (mtp) cc_final: 0.7850 (mtp) REVERT: B 171 TRP cc_start: -0.0221 (p90) cc_final: -0.0613 (p90) REVERT: B 386 ASP cc_start: 0.8720 (p0) cc_final: 0.7896 (p0) REVERT: B 516 MET cc_start: 0.7306 (ttm) cc_final: 0.7082 (ttm) outliers start: 55 outliers final: 37 residues processed: 377 average time/residue: 0.4445 time to fit residues: 282.5708 Evaluate side-chains 349 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 310 time to evaluate : 3.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 323 LYS Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 420 optimal weight: 0.6980 chunk 454 optimal weight: 1.9990 chunk 374 optimal weight: 6.9990 chunk 416 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 337 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 234 GLN A 310 HIS C 168 HIS ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN F 666 HIS ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37249 Z= 0.169 Angle : 0.610 8.764 50505 Z= 0.299 Chirality : 0.043 0.183 5744 Planarity : 0.005 0.062 6557 Dihedral : 8.421 179.756 5164 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 1.39 % Allowed : 11.81 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.13), residues: 4626 helix: 0.60 (0.12), residues: 2012 sheet: -1.99 (0.21), residues: 564 loop : -1.64 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 431 HIS 0.005 0.001 HIS C 319 PHE 0.015 0.001 PHE F 657 TYR 0.023 0.001 TYR D 332 ARG 0.004 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 359 time to evaluate : 4.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6451 (tpt) cc_final: 0.5555 (mpp) REVERT: A 416 ASN cc_start: 0.6826 (OUTLIER) cc_final: 0.6588 (p0) REVERT: A 682 THR cc_start: 0.8269 (m) cc_final: 0.8035 (p) REVERT: A 713 MET cc_start: 0.6632 (tmm) cc_final: 0.5762 (tmm) REVERT: A 723 LEU cc_start: 0.6872 (mt) cc_final: 0.6403 (mt) REVERT: C 440 LEU cc_start: 0.7975 (tp) cc_final: 0.7430 (mt) REVERT: C 473 THR cc_start: 0.8401 (m) cc_final: 0.8158 (p) REVERT: C 735 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7595 (mp) REVERT: E 422 ASP cc_start: 0.7090 (m-30) cc_final: 0.6633 (m-30) REVERT: E 563 TRP cc_start: 0.5345 (p90) cc_final: 0.4718 (p90) REVERT: E 620 SER cc_start: 0.7807 (m) cc_final: 0.7358 (t) REVERT: D 228 GLU cc_start: 0.8544 (tm-30) cc_final: 0.7961 (tm-30) REVERT: D 401 MET cc_start: 0.6990 (tpp) cc_final: 0.6778 (tpp) REVERT: D 625 LEU cc_start: 0.7701 (mp) cc_final: 0.7400 (mp) REVERT: F 431 TRP cc_start: 0.4719 (t-100) cc_final: 0.4308 (p90) REVERT: F 439 MET cc_start: 0.6861 (mtt) cc_final: 0.6647 (mtp) REVERT: F 633 MET cc_start: 0.8135 (mpp) cc_final: 0.7521 (mpp) REVERT: B 171 TRP cc_start: -0.0090 (p90) cc_final: -0.0453 (p90) REVERT: B 208 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6519 (ptt180) REVERT: B 241 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5639 (p0) REVERT: B 381 LEU cc_start: 0.9023 (mt) cc_final: 0.8814 (mp) REVERT: B 386 ASP cc_start: 0.8618 (p0) cc_final: 0.7746 (p0) outliers start: 54 outliers final: 32 residues processed: 393 average time/residue: 0.4319 time to fit residues: 288.3124 Evaluate side-chains 366 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 330 time to evaluate : 3.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 407 HIS Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 415 optimal weight: 8.9990 chunk 316 optimal weight: 30.0000 chunk 218 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 282 optimal weight: 9.9990 chunk 421 optimal weight: 4.9990 chunk 446 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 399 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 310 HIS A 340 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS ** F 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 510 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 37249 Z= 0.371 Angle : 0.737 10.659 50505 Z= 0.365 Chirality : 0.046 0.268 5744 Planarity : 0.006 0.060 6557 Dihedral : 8.682 177.613 5164 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.56 % Favored : 91.42 % Rotamer: Outliers : 2.82 % Allowed : 13.43 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % 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 (0.12), residues: 4626 helix: 0.27 (0.12), residues: 2030 sheet: -2.14 (0.21), residues: 541 loop : -1.87 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.010 0.002 HIS C 407 PHE 0.026 0.002 PHE C 466 TYR 0.032 0.002 TYR A 493 ARG 0.008 0.001 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 320 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6313 (tpt) cc_final: 0.5430 (mpp) REVERT: A 416 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6875 (p0) REVERT: A 713 MET cc_start: 0.6711 (tmm) cc_final: 0.5878 (tmm) REVERT: C 230 MET cc_start: 0.5298 (mpp) cc_final: 0.5001 (mpp) REVERT: C 425 ASP cc_start: 0.8906 (p0) cc_final: 0.8182 (p0) REVERT: C 528 LEU cc_start: 0.8491 (pp) cc_final: 0.8129 (tt) REVERT: C 733 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7678 (mm) REVERT: C 735 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7772 (mp) REVERT: E 563 TRP cc_start: 0.5612 (p90) cc_final: 0.4953 (p90) REVERT: E 620 SER cc_start: 0.7988 (m) cc_final: 0.7619 (t) REVERT: F 75 MET cc_start: 0.4829 (tmm) cc_final: 0.4581 (tmm) REVERT: F 431 TRP cc_start: 0.4725 (t-100) cc_final: 0.4502 (t-100) REVERT: B 171 TRP cc_start: -0.0340 (p90) cc_final: -0.0679 (p90) REVERT: B 386 ASP cc_start: 0.8725 (p0) cc_final: 0.7889 (p0) REVERT: B 440 LEU cc_start: 0.8451 (tp) cc_final: 0.8232 (mt) outliers start: 110 outliers final: 75 residues processed: 399 average time/residue: 0.4691 time to fit residues: 320.6441 Evaluate side-chains 382 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 304 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 682 THR Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 371 optimal weight: 1.9990 chunk 253 optimal weight: 0.7980 chunk 6 optimal weight: 50.0000 chunk 332 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 381 optimal weight: 10.0000 chunk 308 optimal weight: 50.0000 chunk 0 optimal weight: 60.0000 chunk 228 optimal weight: 6.9990 chunk 400 optimal weight: 50.0000 chunk 112 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS D 18 HIS F 510 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37249 Z= 0.281 Angle : 0.675 10.998 50505 Z= 0.331 Chirality : 0.044 0.242 5744 Planarity : 0.005 0.062 6557 Dihedral : 8.608 178.961 5164 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.61 % Favored : 92.37 % Rotamer: Outliers : 2.95 % Allowed : 14.95 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4626 helix: 0.38 (0.12), residues: 2027 sheet: -2.14 (0.21), residues: 543 loop : -1.86 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 558 HIS 0.009 0.001 HIS E 666 PHE 0.019 0.002 PHE B 466 TYR 0.029 0.002 TYR A 493 ARG 0.007 0.000 ARG F 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 317 time to evaluate : 3.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6332 (tpt) cc_final: 0.5444 (mpp) REVERT: A 416 ASN cc_start: 0.7169 (OUTLIER) cc_final: 0.6828 (p0) REVERT: A 702 MET cc_start: 0.6656 (mtt) cc_final: 0.6425 (mtt) REVERT: A 713 MET cc_start: 0.6698 (tmm) cc_final: 0.5850 (tmm) REVERT: A 723 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6362 (mt) REVERT: C 230 MET cc_start: 0.5241 (mpp) cc_final: 0.4960 (mpp) REVERT: C 473 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8317 (m) REVERT: C 528 LEU cc_start: 0.8480 (pp) cc_final: 0.8093 (tt) REVERT: C 733 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7661 (mm) REVERT: C 735 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7678 (mp) REVERT: E 521 GLU cc_start: 0.6052 (pt0) cc_final: 0.5838 (tm-30) REVERT: E 563 TRP cc_start: 0.5558 (p90) cc_final: 0.4590 (p90) REVERT: E 620 SER cc_start: 0.7947 (m) cc_final: 0.7571 (t) REVERT: F 431 TRP cc_start: 0.4750 (t-100) cc_final: 0.4513 (t-100) REVERT: F 439 MET cc_start: 0.6879 (mtt) cc_final: 0.6607 (mtp) REVERT: F 641 LEU cc_start: 0.8726 (mt) cc_final: 0.8495 (mt) REVERT: B 386 ASP cc_start: 0.8794 (p0) cc_final: 0.7906 (p0) outliers start: 115 outliers final: 86 residues processed: 396 average time/residue: 0.4326 time to fit residues: 291.4136 Evaluate side-chains 392 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 301 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 603 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 622 LYS Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 1.9990 chunk 402 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 447 optimal weight: 0.7980 chunk 371 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 234 optimal weight: 20.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS E 666 HIS F 638 GLN ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37249 Z= 0.171 Angle : 0.621 9.935 50505 Z= 0.300 Chirality : 0.043 0.236 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.315 177.608 5164 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.84 % Rotamer: Outliers : 2.34 % Allowed : 16.18 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.03 (0.13), residues: 4626 helix: 0.71 (0.12), residues: 2012 sheet: -1.92 (0.21), residues: 540 loop : -1.73 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP F 558 HIS 0.011 0.001 HIS E 666 PHE 0.041 0.001 PHE F 557 TYR 0.022 0.001 TYR B 768 ARG 0.005 0.000 ARG E 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 340 time to evaluate : 4.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6365 (tpt) cc_final: 0.5486 (mpp) REVERT: A 440 LEU cc_start: 0.7574 (tt) cc_final: 0.7291 (mt) REVERT: A 713 MET cc_start: 0.6753 (tmm) cc_final: 0.5871 (tmm) REVERT: A 723 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6341 (mt) REVERT: C 230 MET cc_start: 0.5378 (mpp) cc_final: 0.5060 (mpp) REVERT: C 440 LEU cc_start: 0.8118 (tp) cc_final: 0.7634 (mt) REVERT: C 473 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8244 (p) REVERT: C 702 MET cc_start: 0.7923 (mpp) cc_final: 0.7678 (mpp) REVERT: C 735 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7590 (mp) REVERT: E 273 LEU cc_start: 0.8082 (mt) cc_final: 0.7830 (mt) REVERT: E 422 ASP cc_start: 0.7173 (m-30) cc_final: 0.6800 (m-30) REVERT: E 563 TRP cc_start: 0.5592 (p90) cc_final: 0.5177 (p90) REVERT: E 620 SER cc_start: 0.7842 (m) cc_final: 0.7493 (t) REVERT: D 427 MET cc_start: 0.8178 (mtp) cc_final: 0.7589 (mtp) REVERT: F 63 TYR cc_start: 0.5118 (m-10) cc_final: 0.4839 (m-10) REVERT: F 431 TRP cc_start: 0.4850 (t-100) cc_final: 0.4605 (t-100) REVERT: B 171 TRP cc_start: -0.0302 (p90) cc_final: -0.0642 (p90) REVERT: B 386 ASP cc_start: 0.8700 (p0) cc_final: 0.7799 (p0) outliers start: 91 outliers final: 67 residues processed: 401 average time/residue: 0.4516 time to fit residues: 308.1161 Evaluate side-chains 382 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 312 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 293 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 430 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 326 optimal weight: 30.0000 chunk 252 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 445 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 271 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 168 HIS ** E 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS ** E 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 37249 Z= 0.499 Angle : 0.850 12.670 50505 Z= 0.424 Chirality : 0.050 0.306 5744 Planarity : 0.006 0.063 6557 Dihedral : 8.956 179.526 5164 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.71 % Favored : 90.27 % Rotamer: Outliers : 3.54 % Allowed : 16.51 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.52 % Twisted General : 0.05 % 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: -1.72 (0.12), residues: 4626 helix: 0.04 (0.11), residues: 2025 sheet: -2.21 (0.22), residues: 502 loop : -2.05 (0.13), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 563 HIS 0.011 0.002 HIS C 726 PHE 0.041 0.003 PHE F 557 TYR 0.034 0.003 TYR A 493 ARG 0.010 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 311 time to evaluate : 4.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6372 (tpt) cc_final: 0.5472 (mpp) REVERT: A 407 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8057 (m-70) REVERT: A 470 THR cc_start: 0.7915 (OUTLIER) cc_final: 0.7272 (m) REVERT: A 723 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6627 (mt) REVERT: A 732 LYS cc_start: 0.7895 (mttp) cc_final: 0.7578 (mtmt) REVERT: C 230 MET cc_start: 0.5224 (mpp) cc_final: 0.4854 (mpp) REVERT: C 528 LEU cc_start: 0.8531 (pp) cc_final: 0.8175 (tt) REVERT: C 631 GLU cc_start: 0.6252 (mm-30) cc_final: 0.6024 (mm-30) REVERT: C 735 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7772 (mp) REVERT: E 543 LEU cc_start: 0.8121 (mt) cc_final: 0.7711 (tt) REVERT: E 563 TRP cc_start: 0.5558 (p90) cc_final: 0.4594 (p90) REVERT: F 75 MET cc_start: 0.4524 (tmm) cc_final: 0.4318 (tmm) REVERT: F 416 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8134 (p0) REVERT: F 431 TRP cc_start: 0.4779 (t-100) cc_final: 0.4405 (t-100) REVERT: B 386 ASP cc_start: 0.8714 (p0) cc_final: 0.7840 (p0) outliers start: 138 outliers final: 101 residues processed: 415 average time/residue: 0.4457 time to fit residues: 312.9806 Evaluate side-chains 406 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 300 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 613 GLU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 467 PHE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 564 GLU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 251 LYS Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 469 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 520 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 275 optimal weight: 0.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 86 optimal weight: 8.9990 chunk 283 optimal weight: 0.9980 chunk 303 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 350 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS E 666 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37249 Z= 0.189 Angle : 0.653 10.177 50505 Z= 0.316 Chirality : 0.044 0.222 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.490 179.005 5164 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.47 % Rotamer: Outliers : 2.54 % Allowed : 17.36 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.16 (0.13), residues: 4626 helix: 0.58 (0.12), residues: 2016 sheet: -1.91 (0.22), residues: 521 loop : -1.82 (0.14), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 558 HIS 0.019 0.001 HIS E 666 PHE 0.028 0.001 PHE A 451 TYR 0.044 0.001 TYR B 768 ARG 0.007 0.000 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 337 time to evaluate : 4.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6340 (tpt) cc_final: 0.5457 (mpp) REVERT: A 409 MET cc_start: 0.8840 (tpt) cc_final: 0.8211 (mmm) REVERT: A 470 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7146 (m) REVERT: A 713 MET cc_start: 0.6706 (tmm) cc_final: 0.5842 (tmm) REVERT: A 723 LEU cc_start: 0.6978 (mt) cc_final: 0.6393 (mt) REVERT: A 732 LYS cc_start: 0.7750 (mttp) cc_final: 0.7389 (mtmm) REVERT: C 230 MET cc_start: 0.5466 (mpp) cc_final: 0.5084 (mpp) REVERT: C 440 LEU cc_start: 0.8184 (tp) cc_final: 0.7716 (mt) REVERT: C 702 MET cc_start: 0.7883 (mpp) cc_final: 0.7514 (mpp) REVERT: C 735 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7527 (mp) REVERT: E 273 LEU cc_start: 0.8093 (mt) cc_final: 0.7867 (mt) REVERT: E 409 MET cc_start: 0.7805 (tpp) cc_final: 0.7468 (mpp) REVERT: E 422 ASP cc_start: 0.7136 (m-30) cc_final: 0.6845 (m-30) REVERT: E 563 TRP cc_start: 0.5539 (p90) cc_final: 0.4651 (p90) REVERT: E 620 SER cc_start: 0.7953 (m) cc_final: 0.7512 (t) REVERT: D 698 MET cc_start: 0.3977 (mmm) cc_final: 0.3504 (mmm) REVERT: F 75 MET cc_start: 0.4566 (tmm) cc_final: 0.4339 (tmm) REVERT: F 431 TRP cc_start: 0.4700 (t-100) cc_final: 0.4265 (t-100) REVERT: B 386 ASP cc_start: 0.8655 (p0) cc_final: 0.7764 (p0) outliers start: 99 outliers final: 75 residues processed: 399 average time/residue: 0.4439 time to fit residues: 298.1355 Evaluate side-chains 396 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 319 time to evaluate : 4.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 633 MET Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 405 optimal weight: 9.9990 chunk 426 optimal weight: 4.9990 chunk 389 optimal weight: 10.0000 chunk 414 optimal weight: 0.6980 chunk 249 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 374 optimal weight: 5.9990 chunk 392 optimal weight: 20.0000 chunk 413 optimal weight: 0.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 598 GLN ** E 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 HIS D 659 ASN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37249 Z= 0.238 Angle : 0.674 12.063 50505 Z= 0.325 Chirality : 0.044 0.264 5744 Planarity : 0.005 0.063 6557 Dihedral : 8.438 179.849 5164 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.76 % Favored : 92.22 % Rotamer: Outliers : 2.34 % Allowed : 17.67 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.13 (0.13), residues: 4626 helix: 0.60 (0.12), residues: 2018 sheet: -1.93 (0.22), residues: 508 loop : -1.80 (0.14), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 558 HIS 0.007 0.001 HIS E 666 PHE 0.021 0.001 PHE A 451 TYR 0.022 0.001 TYR F 63 ARG 0.007 0.000 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 317 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6373 (tpt) cc_final: 0.5482 (mpp) REVERT: A 407 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.8126 (m-70) REVERT: A 409 MET cc_start: 0.8845 (tpt) cc_final: 0.8219 (mmm) REVERT: A 440 LEU cc_start: 0.7619 (tt) cc_final: 0.7346 (mt) REVERT: A 713 MET cc_start: 0.6719 (tmm) cc_final: 0.5852 (tmm) REVERT: A 723 LEU cc_start: 0.7023 (mt) cc_final: 0.6397 (mt) REVERT: A 732 LYS cc_start: 0.7796 (mttp) cc_final: 0.7523 (mtmt) REVERT: C 230 MET cc_start: 0.5394 (mpp) cc_final: 0.5002 (mpp) REVERT: C 440 LEU cc_start: 0.8168 (tp) cc_final: 0.7718 (mt) REVERT: C 735 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7583 (mp) REVERT: E 422 ASP cc_start: 0.7192 (m-30) cc_final: 0.6885 (m-30) REVERT: E 563 TRP cc_start: 0.5554 (p90) cc_final: 0.4641 (p90) REVERT: E 620 SER cc_start: 0.7981 (m) cc_final: 0.7551 (t) REVERT: D 698 MET cc_start: 0.4165 (mmm) cc_final: 0.3656 (mmm) REVERT: F 75 MET cc_start: 0.4419 (tmm) cc_final: 0.4184 (tmm) REVERT: F 431 TRP cc_start: 0.4699 (t-100) cc_final: 0.4238 (t-100) REVERT: F 485 MET cc_start: 0.6237 (mmm) cc_final: 0.5762 (mmp) REVERT: B 386 ASP cc_start: 0.8613 (p0) cc_final: 0.7735 (p0) outliers start: 91 outliers final: 80 residues processed: 379 average time/residue: 0.4401 time to fit residues: 281.5107 Evaluate side-chains 396 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 314 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 699 ASP Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 272 optimal weight: 4.9990 chunk 438 optimal weight: 7.9990 chunk 267 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 305 optimal weight: 0.0050 chunk 460 optimal weight: 9.9990 chunk 423 optimal weight: 4.9990 chunk 366 optimal weight: 0.4980 chunk 38 optimal weight: 9.9990 chunk 283 optimal weight: 0.8980 chunk 224 optimal weight: 6.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 666 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37249 Z= 0.189 Angle : 0.656 12.257 50505 Z= 0.314 Chirality : 0.044 0.225 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.299 178.004 5164 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.81 % Favored : 93.17 % Rotamer: Outliers : 2.11 % Allowed : 17.93 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -0.99 (0.13), residues: 4626 helix: 0.72 (0.12), residues: 2013 sheet: -1.89 (0.22), residues: 514 loop : -1.70 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 558 HIS 0.013 0.001 HIS E 666 PHE 0.030 0.001 PHE D 203 TYR 0.021 0.001 TYR F 63 ARG 0.007 0.000 ARG C 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 325 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.6395 (tpt) cc_final: 0.5511 (mpp) REVERT: A 407 HIS cc_start: 0.8351 (OUTLIER) cc_final: 0.8105 (m-70) REVERT: A 409 MET cc_start: 0.8834 (tpt) cc_final: 0.8222 (mmm) REVERT: A 440 LEU cc_start: 0.7621 (tt) cc_final: 0.7360 (mt) REVERT: A 563 TRP cc_start: 0.4027 (m100) cc_final: 0.3462 (m100) REVERT: A 713 MET cc_start: 0.6724 (tmm) cc_final: 0.5865 (tmm) REVERT: A 723 LEU cc_start: 0.6912 (mt) cc_final: 0.6292 (mt) REVERT: A 732 LYS cc_start: 0.7833 (mttp) cc_final: 0.7591 (mtmt) REVERT: C 230 MET cc_start: 0.5440 (mpp) cc_final: 0.5058 (mpp) REVERT: C 440 LEU cc_start: 0.8035 (tp) cc_final: 0.7581 (mt) REVERT: C 512 ARG cc_start: 0.7484 (ptt90) cc_final: 0.6959 (mtm180) REVERT: C 735 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7486 (mp) REVERT: E 273 LEU cc_start: 0.8099 (mt) cc_final: 0.7874 (mt) REVERT: E 422 ASP cc_start: 0.7190 (m-30) cc_final: 0.6945 (m-30) REVERT: E 563 TRP cc_start: 0.5454 (p90) cc_final: 0.4563 (p90) REVERT: E 620 SER cc_start: 0.7878 (m) cc_final: 0.7464 (t) REVERT: E 718 VAL cc_start: 0.6517 (OUTLIER) cc_final: 0.5380 (m) REVERT: F 75 MET cc_start: 0.4419 (tmm) cc_final: 0.4178 (tmm) REVERT: F 409 MET cc_start: 0.7727 (mpp) cc_final: 0.7501 (mpp) REVERT: F 431 TRP cc_start: 0.4751 (t-100) cc_final: 0.4278 (t-100) REVERT: F 485 MET cc_start: 0.6339 (mmm) cc_final: 0.5836 (mmp) REVERT: F 633 MET cc_start: 0.8150 (mpp) cc_final: 0.7435 (mpp) REVERT: B 262 VAL cc_start: 0.8678 (t) cc_final: 0.8403 (t) REVERT: B 386 ASP cc_start: 0.8586 (p0) cc_final: 0.7764 (p0) outliers start: 82 outliers final: 73 residues processed: 378 average time/residue: 0.4386 time to fit residues: 281.0948 Evaluate side-chains 389 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 313 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 733 ILE Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 449 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 613 GLU Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 625 LEU Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 735 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 427 MET Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 666 HIS Chi-restraints excluded: chain E residue 700 ILE Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 735 LEU Chi-restraints excluded: chain E residue 761 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 397 TYR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 617 VAL Chi-restraints excluded: chain D residue 658 TYR Chi-restraints excluded: chain D residue 662 ASP Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 284 THR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 416 ASN Chi-restraints excluded: chain F residue 642 THR Chi-restraints excluded: chain F residue 702 MET Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain B residue 247 GLU Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 461 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 726 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 291 optimal weight: 7.9990 chunk 390 optimal weight: 0.0470 chunk 112 optimal weight: 4.9990 chunk 337 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 367 optimal weight: 8.9990 chunk 153 optimal weight: 0.4980 chunk 376 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 666 HIS F 18 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.183808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.136723 restraints weight = 87613.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.127660 restraints weight = 76689.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.128573 restraints weight = 71529.273| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37249 Z= 0.226 Angle : 0.669 12.100 50505 Z= 0.321 Chirality : 0.044 0.231 5744 Planarity : 0.005 0.064 6557 Dihedral : 8.293 178.524 5164 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 2.39 % Allowed : 17.98 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.14 % Twisted General : 0.02 % 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: -1.00 (0.13), residues: 4626 helix: 0.71 (0.12), residues: 2013 sheet: -1.89 (0.22), residues: 514 loop : -1.70 (0.14), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 558 HIS 0.007 0.001 HIS E 666 PHE 0.016 0.001 PHE A 451 TYR 0.025 0.001 TYR D 332 ARG 0.007 0.000 ARG C 512 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7347.48 seconds wall clock time: 132 minutes 17.63 seconds (7937.63 seconds total)