Starting phenix.real_space_refine on Thu Jul 25 21:40:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/07_2024/7yuw_34113.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 8 5.49 5 S 105 5.16 5 C 19230 2.51 5 N 5355 2.21 5 O 5785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 767": "OE1" <-> "OE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C GLU 749": "OE1" <-> "OE2" Residue "C GLU 755": "OE1" <-> "OE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D GLU 631": "OE1" <-> "OE2" Residue "D GLU 635": "OE1" <-> "OE2" Residue "D GLU 720": "OE1" <-> "OE2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D GLU 745": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "E GLU 517": "OE1" <-> "OE2" Residue "E GLU 631": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 30483 Number of models: 1 Model: "" Number of chains: 9 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: "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: "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: "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: "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: "A" 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} 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: "D" 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: 16.45, per 1000 atoms: 0.54 Number of scatterers: 30483 At special positions: 0 Unit cell: (195.98, 157.44, 168.92, 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 105 16.00 P 8 15.00 O 5785 8.00 N 5355 7.00 C 19230 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: 12.21 Conformation dependent library (CDL) restraints added in 5.8 seconds 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7180 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 39 sheets defined 46.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 30 through 40 removed outlier: 4.294A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.609A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 235 removed outlier: 3.736A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.581A pdb=" N VAL A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 283 through 296 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.505A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 removed outlier: 4.236A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.904A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 4.174A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'A' and resid 494 through 506 removed outlier: 3.554A pdb=" N LEU A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 513 Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.019A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 645 removed outlier: 3.653A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 removed outlier: 3.675A pdb=" N ARG A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 4.114A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.651A pdb=" N LEU A 746 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 removed outlier: 3.641A pdb=" N LEU A 754 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.985A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 removed outlier: 3.718A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.509A pdb=" N ASP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 62' Processing helix chain 'B' and resid 117 through 138 removed outlier: 3.806A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.812A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 153 " --> pdb=" O GLU B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 149 through 153' Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.680A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS B 168 " --> pdb=" O THR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.866A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 237 removed outlier: 4.134A pdb=" N TYR B 224 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 283 through 296 Processing helix chain 'B' and resid 310 through 319 removed outlier: 3.935A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.583A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 removed outlier: 3.920A pdb=" N ILE B 390 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 434 through 440 removed outlier: 4.356A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.842A pdb=" N ALA B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.755A 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 631 through 646 Processing helix chain 'B' and resid 647 through 651 removed outlier: 3.710A pdb=" N TYR B 651 " --> pdb=" O THR B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.501A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 744 removed outlier: 3.550A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 767 removed outlier: 3.813A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.889A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 146 through 152 removed outlier: 3.704A pdb=" N GLU C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.731A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 163 " --> pdb=" O ALA C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.705A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 236 removed outlier: 3.670A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 removed outlier: 3.543A pdb=" N ARG C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.816A pdb=" N THR C 311 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 360 through 371 Processing helix chain 'C' and resid 386 through 391 removed outlier: 3.607A pdb=" N ILE C 390 " --> pdb=" O ASP C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 434 through 444 removed outlier: 4.398A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.960A pdb=" N ASP C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 503 Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 523 through 535 removed outlier: 3.755A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 535 " --> pdb=" O ILE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.673A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.874A 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 727 Processing helix chain 'C' and resid 736 through 738 No H-bonds generated for 'chain 'C' and resid 736 through 738' Processing helix chain 'C' and resid 739 through 744 removed outlier: 3.638A pdb=" N GLU C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 770 Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.720A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 137 removed outlier: 4.274A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.669A pdb=" N LYS D 153 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.543A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 removed outlier: 3.570A pdb=" N ILE D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 238 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 307 through 318 removed outlier: 3.519A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 338 removed outlier: 3.514A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 removed outlier: 4.140A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 4.201A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.506A pdb=" N ASP D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.199A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 483 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 506 through 514 removed outlier: 3.984A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.978A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.536A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.849A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 removed outlier: 3.547A pdb=" N GLU D 589 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR D 590 " --> pdb=" O LYS D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 586 through 590' Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.500A pdb=" N HIS D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 660 removed outlier: 3.550A pdb=" N LYS D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 656 through 660' Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 724 removed outlier: 3.525A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 744 removed outlier: 5.054A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 770 removed outlier: 4.120A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 40 Processing helix chain 'E' and resid 58 through 62 Processing helix chain 'E' and resid 117 through 139 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.804A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 233 removed outlier: 4.040A pdb=" N ARG E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.543A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 4.619A 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 295 removed outlier: 3.581A pdb=" N GLU E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 316 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 360 through 373 removed outlier: 3.527A pdb=" N LEU E 364 " --> pdb=" O GLY E 360 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.616A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 435 through 444 Processing helix chain 'E' and resid 444 through 449 removed outlier: 3.558A pdb=" N ASN E 449 " --> pdb=" O PRO E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 494 through 514 removed outlier: 5.176A pdb=" N TRP E 507 " --> pdb=" O ARG E 503 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 523 through 535 removed outlier: 3.568A pdb=" N ILE E 527 " --> pdb=" O THR E 523 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.700A pdb=" N GLU E 560 " --> pdb=" O LYS E 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 584 through 588 removed outlier: 4.336A pdb=" N LYS E 587 " --> pdb=" O ARG E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 647 removed outlier: 3.894A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 651 Processing helix chain 'E' and resid 656 through 659 removed outlier: 3.528A pdb=" N ASN E 659 " --> pdb=" O ASP E 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 656 through 659' Processing helix chain 'E' and resid 679 through 691 Processing helix chain 'E' and resid 717 through 728 Processing helix chain 'E' and resid 738 through 743 removed outlier: 4.577A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 768 Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23 removed outlier: 7.357A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 377 through 380 removed outlier: 6.222A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.294A 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 596 through 601 removed outlier: 3.617A pdb=" N VAL A 665 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.907A pdb=" N ALA A 701 " --> pdb=" O VAL A 734 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 735 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 759 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.791A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 25 removed outlier: 7.056A pdb=" N LEU B 82 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ARG B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 84 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N VAL B 86 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 72 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 98 removed outlier: 4.468A pdb=" N ARG B 104 " --> pdb=" O ILE B 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 470 through 471 removed outlier: 5.595A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 378 removed outlier: 6.756A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 597 through 603 removed outlier: 3.731A pdb=" N ALA B 597 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 599 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 614 through 615 removed outlier: 6.889A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.540A pdb=" N VAL B 734 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.583A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 20 through 22 removed outlier: 5.382A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 354 removed outlier: 6.434A pdb=" N VAL C 352 " --> pdb=" O ILE C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.608A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 520 through 522 removed outlier: 3.575A pdb=" N ILE C 569 " --> pdb=" O GLU C 521 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 592 through 593 removed outlier: 3.805A pdb=" N GLN C 593 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 597 through 601 removed outlier: 4.161A pdb=" N ALA C 597 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 665 " --> pdb=" O SER C 624 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 705 through 707 removed outlier: 3.550A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.464A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.696A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN D 83 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ALA D 74 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AC9, first strand: chain 'D' and resid 377 through 378 removed outlier: 3.725A pdb=" N HIS D 377 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 420 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AD2, first strand: chain 'D' and resid 596 through 598 removed outlier: 3.525A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 612 " --> pdb=" O ALA D 597 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS D 622 " --> pdb=" O VAL D 661 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 601 through 603 removed outlier: 3.667A pdb=" N THR D 608 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 701 through 702 removed outlier: 7.219A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 705 through 707 Processing sheet with id=AD6, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.246A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 104 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.246A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 104 " --> pdb=" O ILE E 98 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.671A pdb=" N ASP E 422 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.780A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'E' and resid 597 through 603 removed outlier: 4.224A pdb=" N ALA E 601 " --> pdb=" O THR E 608 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR E 608 " --> pdb=" O ALA E 601 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 603 " --> pdb=" O GLY E 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 701 through 702 removed outlier: 6.398A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 705 through 707 removed outlier: 3.635A pdb=" N GLU E 705 " --> pdb=" O MET E 713 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS E 711 " --> pdb=" O SER E 707 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3672 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.57 Time building geometry restraints manager: 13.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8610 1.33 - 1.45: 4540 1.45 - 1.57: 17664 1.57 - 1.70: 12 1.70 - 1.82: 210 Bond restraints: 31036 Sorted by residual: bond pdb=" N LEU E 246 " pdb=" CA LEU E 246 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.00e+01 bond pdb=" N ILE E 233 " pdb=" CA ILE E 233 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.33e+00 bond pdb=" N ASP D 241 " pdb=" CA ASP D 241 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.27e+00 bond pdb=" N ASP B 245 " pdb=" CA ASP B 245 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.88e+00 bond pdb=" N LEU C 243 " pdb=" CA LEU C 243 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.71e+00 ... (remaining 31031 not shown) Histogram of bond angle deviations from ideal: 96.70 - 104.61: 695 104.61 - 112.52: 16256 112.52 - 120.43: 13347 120.43 - 128.34: 11573 128.34 - 136.25: 209 Bond angle restraints: 42080 Sorted by residual: angle pdb=" N VAL D 762 " pdb=" CA VAL D 762 " pdb=" C VAL D 762 " ideal model delta sigma weight residual 111.91 105.57 6.34 8.90e-01 1.26e+00 5.08e+01 angle pdb=" N ILE B 308 " pdb=" CA ILE B 308 " pdb=" C ILE B 308 " ideal model delta sigma weight residual 113.47 106.60 6.87 1.01e+00 9.80e-01 4.63e+01 angle pdb=" N LEU A 246 " pdb=" CA LEU A 246 " pdb=" C LEU A 246 " ideal model delta sigma weight residual 111.82 104.76 7.06 1.16e+00 7.43e-01 3.70e+01 angle pdb=" C ARG C 250 " pdb=" N LYS C 251 " pdb=" CA LYS C 251 " ideal model delta sigma weight residual 120.29 112.48 7.81 1.42e+00 4.96e-01 3.03e+01 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 111.48 107.05 4.43 9.40e-01 1.13e+00 2.22e+01 ... (remaining 42075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 18826 33.01 - 66.02: 269 66.02 - 99.04: 51 99.04 - 132.05: 2 132.05 - 165.06: 1 Dihedral angle restraints: 19149 sinusoidal: 7994 harmonic: 11155 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 -133.15 -46.85 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" CA ASP C 51 " pdb=" C ASP C 51 " pdb=" N PRO C 52 " pdb=" CA PRO C 52 " ideal model delta harmonic sigma weight residual 180.00 -134.99 -45.01 0 5.00e+00 4.00e-02 8.10e+01 dihedral pdb=" CA ASP A 51 " pdb=" C ASP A 51 " pdb=" N PRO A 52 " pdb=" CA PRO A 52 " ideal model delta harmonic sigma weight residual 180.00 -144.45 -35.55 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 19146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4126 0.067 - 0.134: 625 0.134 - 0.201: 32 0.201 - 0.267: 2 0.267 - 0.334: 1 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CB ILE B 379 " pdb=" CA ILE B 379 " pdb=" CG1 ILE B 379 " pdb=" CG2 ILE B 379 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA LEU A 246 " pdb=" N LEU A 246 " pdb=" C LEU A 246 " pdb=" CB LEU A 246 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE E 233 " pdb=" CA ILE E 233 " pdb=" CG1 ILE E 233 " pdb=" CG2 ILE E 233 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 4783 not shown) Planarity restraints: 5464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 603 " -0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO D 604 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO D 604 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 604 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 51 " 0.058 5.00e-02 4.00e+02 8.90e-02 1.27e+01 pdb=" N PRO A 52 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 444 " 0.053 5.00e-02 4.00e+02 8.17e-02 1.07e+01 pdb=" N PRO D 445 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO D 445 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 445 " 0.044 5.00e-02 4.00e+02 ... (remaining 5461 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 779 2.69 - 3.25: 30615 3.25 - 3.80: 47749 3.80 - 4.35: 63197 4.35 - 4.90: 102430 Nonbonded interactions: 244770 Sorted by model distance: nonbonded pdb=" O TYR C 493 " pdb=" OG1 THR C 494 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR E 626 " pdb=" O VAL E 665 " model vdw 2.175 2.440 nonbonded pdb=" O PRO B 402 " pdb=" NH2 ARG C 432 " model vdw 2.182 2.520 nonbonded pdb=" O GLN E 277 " pdb=" OG1 THR E 284 " model vdw 2.186 2.440 nonbonded pdb=" O TYR B 493 " pdb=" OG1 THR B 494 " model vdw 2.188 2.440 ... (remaining 244765 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' } 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: 1.870 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: 1.370 Check model and map are aligned: 0.240 Set scattering table: 0.340 Process input model: 80.990 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.160 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 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 : 0.004 0.055 31036 Z= 0.251 Angle : 0.764 9.388 42080 Z= 0.438 Chirality : 0.046 0.334 4786 Planarity : 0.006 0.093 5464 Dihedral : 12.959 165.062 11969 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.22 % Favored : 91.73 % Rotamer: Outliers : 0.15 % Allowed : 0.40 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.13), residues: 3855 helix: -0.04 (0.13), residues: 1649 sheet: -2.60 (0.23), residues: 455 loop : -2.33 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 292 HIS 0.005 0.001 HIS E 377 PHE 0.011 0.001 PHE E 557 TYR 0.022 0.001 TYR A 493 ARG 0.008 0.000 ARG E 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 348 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3422 (p90) cc_final: 0.2830 (p90) REVERT: B 85 MET cc_start: 0.4867 (mmt) cc_final: 0.4462 (mmt) REVERT: B 488 ILE cc_start: 0.7868 (mm) cc_final: 0.7377 (mt) REVERT: C 378 ARG cc_start: 0.8460 (tmm-80) cc_final: 0.7867 (ttt180) REVERT: D 419 ILE cc_start: 0.8583 (mm) cc_final: 0.8374 (mm) REVERT: E 85 MET cc_start: 0.5286 (mpp) cc_final: 0.4082 (mpp) REVERT: E 258 MET cc_start: 0.4479 (tpp) cc_final: 0.4174 (tpp) outliers start: 5 outliers final: 1 residues processed: 353 average time/residue: 0.3819 time to fit residues: 224.6894 Evaluate side-chains 269 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 20.0000 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 0.0040 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 0.0470 chunk 155 optimal weight: 30.0000 chunk 301 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 224 optimal weight: 0.6980 chunk 349 optimal weight: 0.2980 overall best weight: 1.0092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 340 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 GLN E 666 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31036 Z= 0.184 Angle : 0.642 8.584 42080 Z= 0.319 Chirality : 0.044 0.280 4786 Planarity : 0.005 0.061 5464 Dihedral : 7.399 177.994 4301 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.81 % Favored : 92.14 % Rotamer: Outliers : 0.83 % Allowed : 6.81 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3855 helix: 0.17 (0.13), residues: 1690 sheet: -2.42 (0.22), residues: 451 loop : -2.32 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 298 HIS 0.005 0.001 HIS E 377 PHE 0.019 0.001 PHE C 657 TYR 0.032 0.001 TYR C 768 ARG 0.008 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 314 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3015 (p90) cc_final: 0.2349 (p90) REVERT: B 85 MET cc_start: 0.5005 (mmt) cc_final: 0.4636 (mmt) REVERT: B 488 ILE cc_start: 0.7894 (mm) cc_final: 0.7395 (mt) REVERT: B 496 MET cc_start: 0.7874 (tpp) cc_final: 0.7673 (tpp) REVERT: B 566 LEU cc_start: 0.7813 (tp) cc_final: 0.7470 (tt) REVERT: C 160 MET cc_start: 0.3946 (tmm) cc_final: 0.3551 (mmt) REVERT: C 230 MET cc_start: 0.7626 (tmm) cc_final: 0.7236 (tmm) REVERT: C 378 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.7864 (ttt180) REVERT: D 419 ILE cc_start: 0.8515 (mm) cc_final: 0.8192 (mm) REVERT: E 85 MET cc_start: 0.5408 (mpp) cc_final: 0.4244 (mpp) REVERT: E 258 MET cc_start: 0.4505 (tpp) cc_final: 0.4184 (tpp) REVERT: E 535 THR cc_start: 0.6738 (p) cc_final: 0.6534 (p) REVERT: E 631 GLU cc_start: 0.6499 (tp30) cc_final: 0.5661 (tp30) outliers start: 27 outliers final: 14 residues processed: 328 average time/residue: 0.3914 time to fit residues: 213.1078 Evaluate side-chains 291 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 277 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 0.0470 chunk 238 optimal weight: 20.0000 chunk 96 optimal weight: 40.0000 chunk 350 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 347 optimal weight: 30.0000 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 GLN A 598 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31036 Z= 0.283 Angle : 0.671 8.294 42080 Z= 0.332 Chirality : 0.045 0.293 4786 Planarity : 0.005 0.062 5464 Dihedral : 7.280 163.903 4299 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.87 % Favored : 91.08 % Rotamer: Outliers : 1.45 % Allowed : 9.80 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.13), residues: 3855 helix: 0.15 (0.13), residues: 1680 sheet: -2.43 (0.23), residues: 443 loop : -2.36 (0.14), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 292 HIS 0.006 0.001 HIS B 319 PHE 0.024 0.002 PHE E 557 TYR 0.035 0.002 TYR C 768 ARG 0.008 0.000 ARG B 484 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 283 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.4991 (mmt) cc_final: 0.4646 (mmt) REVERT: B 316 ASP cc_start: 0.7048 (m-30) cc_final: 0.6846 (m-30) REVERT: C 160 MET cc_start: 0.3894 (tmm) cc_final: 0.3535 (mmt) REVERT: C 262 VAL cc_start: 0.7775 (OUTLIER) cc_final: 0.7535 (t) REVERT: C 625 LEU cc_start: 0.8105 (mt) cc_final: 0.7894 (mt) REVERT: D 229 GLN cc_start: 0.6946 (tp-100) cc_final: 0.6536 (tt0) REVERT: D 426 LYS cc_start: 0.8476 (mppt) cc_final: 0.8234 (tttt) REVERT: E 85 MET cc_start: 0.5367 (mpp) cc_final: 0.4294 (mpp) outliers start: 47 outliers final: 35 residues processed: 311 average time/residue: 0.3669 time to fit residues: 195.2967 Evaluate side-chains 295 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 259 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 482 LEU 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 613 GLU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 235 optimal weight: 40.0000 chunk 351 optimal weight: 20.0000 chunk 372 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS A 475 GLN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 340 GLN ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 666 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 31036 Z= 0.411 Angle : 0.768 10.616 42080 Z= 0.380 Chirality : 0.048 0.286 4786 Planarity : 0.006 0.068 5464 Dihedral : 7.486 153.332 4299 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.25 % Favored : 89.68 % Rotamer: Outliers : 2.53 % Allowed : 11.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3855 helix: -0.15 (0.13), residues: 1681 sheet: -2.34 (0.25), residues: 410 loop : -2.49 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 563 HIS 0.008 0.002 HIS B 319 PHE 0.030 0.002 PHE E 557 TYR 0.030 0.002 TYR C 768 ARG 0.007 0.001 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 292 time to evaluate : 3.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6376 (mm-30) REVERT: B 85 MET cc_start: 0.4975 (mmt) cc_final: 0.4693 (mmt) REVERT: B 490 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7298 (mt) REVERT: C 262 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.7605 (t) REVERT: C 439 MET cc_start: 0.7617 (mmm) cc_final: 0.7344 (mmm) REVERT: C 568 THR cc_start: 0.8549 (m) cc_final: 0.8146 (p) REVERT: C 625 LEU cc_start: 0.8316 (mt) cc_final: 0.8093 (mt) REVERT: D 229 GLN cc_start: 0.6912 (tp-100) cc_final: 0.6618 (tt0) REVERT: D 277 GLN cc_start: 0.6455 (pt0) cc_final: 0.6234 (mt0) REVERT: D 390 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7950 (mt) REVERT: D 426 LYS cc_start: 0.8516 (mppt) cc_final: 0.8300 (tttt) REVERT: D 631 GLU cc_start: 0.6574 (tp30) cc_final: 0.6020 (tp30) REVERT: D 635 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5940 (mm-30) REVERT: E 85 MET cc_start: 0.5178 (mpp) cc_final: 0.4506 (mpp) REVERT: E 258 MET cc_start: 0.3864 (tpp) cc_final: 0.3468 (tpp) REVERT: E 265 LYS cc_start: 0.4180 (pttt) cc_final: 0.3213 (mtpp) REVERT: E 437 SER cc_start: 0.5449 (p) cc_final: 0.5243 (t) REVERT: E 483 ASP cc_start: 0.7420 (t0) cc_final: 0.7218 (t0) REVERT: E 546 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6211 (pp20) REVERT: E 713 MET cc_start: 0.7296 (ttp) cc_final: 0.7033 (mtm) outliers start: 82 outliers final: 52 residues processed: 346 average time/residue: 0.3650 time to fit residues: 213.5974 Evaluate side-chains 322 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 309 ASN Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 490 ILE 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 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 40.0000 chunk 211 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 277 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 317 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 0.9990 chunk 334 optimal weight: 5.9990 chunk 93 optimal weight: 50.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31036 Z= 0.239 Angle : 0.666 8.518 42080 Z= 0.327 Chirality : 0.045 0.306 4786 Planarity : 0.005 0.075 5464 Dihedral : 7.147 146.294 4299 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.40 % Favored : 91.52 % Rotamer: Outliers : 2.40 % Allowed : 13.68 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % 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: -1.92 (0.14), residues: 3855 helix: 0.05 (0.13), residues: 1692 sheet: -2.45 (0.24), residues: 422 loop : -2.32 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 602 HIS 0.005 0.001 HIS E 377 PHE 0.028 0.001 PHE E 557 TYR 0.025 0.001 TYR C 768 ARG 0.007 0.000 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 287 time to evaluate : 3.634 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 247 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6233 (mm-30) REVERT: A 331 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: B 75 MET cc_start: 0.0392 (mmm) cc_final: -0.0012 (mmm) REVERT: B 85 MET cc_start: 0.5007 (mmt) cc_final: 0.4734 (mmt) REVERT: B 754 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.6914 (mt) REVERT: C 160 MET cc_start: 0.3952 (tmm) cc_final: 0.3383 (mpp) REVERT: C 262 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7558 (t) REVERT: C 494 THR cc_start: 0.7680 (p) cc_final: 0.7478 (p) REVERT: C 568 THR cc_start: 0.8512 (m) cc_final: 0.8096 (p) REVERT: C 625 LEU cc_start: 0.8174 (mt) cc_final: 0.7973 (mt) REVERT: D 229 GLN cc_start: 0.6729 (tp-100) cc_final: 0.6528 (tt0) REVERT: D 277 GLN cc_start: 0.6509 (pt0) cc_final: 0.6244 (mt0) REVERT: D 390 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7861 (mt) REVERT: D 426 LYS cc_start: 0.8524 (mppt) cc_final: 0.8187 (tttt) REVERT: D 631 GLU cc_start: 0.6471 (tp30) cc_final: 0.6162 (tp30) REVERT: E 85 MET cc_start: 0.5224 (mpp) cc_final: 0.4168 (mpp) REVERT: E 258 MET cc_start: 0.3677 (tpp) cc_final: 0.3267 (tpp) REVERT: E 265 LYS cc_start: 0.4273 (pttt) cc_final: 0.3146 (mmmt) REVERT: E 713 MET cc_start: 0.7181 (ttp) cc_final: 0.6966 (mtm) outliers start: 78 outliers final: 46 residues processed: 341 average time/residue: 0.3771 time to fit residues: 215.8945 Evaluate side-chains 319 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 268 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 3.9990 chunk 335 optimal weight: 0.3980 chunk 73 optimal weight: 7.9990 chunk 218 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 372 optimal weight: 10.0000 chunk 309 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN B 454 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6296 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31036 Z= 0.168 Angle : 0.625 9.062 42080 Z= 0.304 Chirality : 0.043 0.332 4786 Planarity : 0.005 0.073 5464 Dihedral : 6.635 123.040 4299 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.39 % Favored : 92.56 % Rotamer: Outliers : 1.88 % Allowed : 14.67 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3855 helix: 0.26 (0.13), residues: 1697 sheet: -2.34 (0.23), residues: 437 loop : -2.11 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 65 HIS 0.007 0.001 HIS A 377 PHE 0.023 0.001 PHE E 557 TYR 0.031 0.001 TYR C 768 ARG 0.008 0.000 ARG B 512 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 302 time to evaluate : 3.264 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 247 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6161 (mm-30) REVERT: A 331 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: B 75 MET cc_start: 0.0341 (mmm) cc_final: -0.0029 (mmm) REVERT: B 85 MET cc_start: 0.5001 (mmt) cc_final: 0.4735 (mmt) REVERT: B 754 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6700 (mt) REVERT: C 160 MET cc_start: 0.3898 (tmm) cc_final: 0.3445 (mmt) REVERT: C 230 MET cc_start: 0.7571 (tmm) cc_final: 0.7342 (tmm) REVERT: C 262 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7572 (t) REVERT: C 378 ARG cc_start: 0.8431 (tmm-80) cc_final: 0.7973 (ttt-90) REVERT: C 496 MET cc_start: 0.7916 (mmm) cc_final: 0.7373 (mmm) REVERT: C 568 THR cc_start: 0.8474 (m) cc_final: 0.8058 (p) REVERT: D 262 VAL cc_start: 0.7349 (t) cc_final: 0.7086 (t) REVERT: D 277 GLN cc_start: 0.6489 (pt0) cc_final: 0.5999 (mt0) REVERT: D 390 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7765 (mt) REVERT: D 426 LYS cc_start: 0.8365 (mppt) cc_final: 0.8050 (tttt) REVERT: D 440 LEU cc_start: 0.7682 (mt) cc_final: 0.7436 (mt) REVERT: E 85 MET cc_start: 0.5026 (mpp) cc_final: 0.4462 (mpp) REVERT: E 258 MET cc_start: 0.3703 (tpp) cc_final: 0.3363 (tpp) REVERT: E 698 MET cc_start: 0.4032 (mtm) cc_final: 0.3782 (mtt) outliers start: 61 outliers final: 38 residues processed: 342 average time/residue: 0.4213 time to fit residues: 241.0433 Evaluate side-chains 322 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 279 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 212 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 313 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 371 optimal weight: 3.9990 chunk 232 optimal weight: 0.0020 chunk 226 optimal weight: 5.9990 chunk 171 optimal weight: 40.0000 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN E 659 ASN ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6332 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31036 Z= 0.204 Angle : 0.634 8.742 42080 Z= 0.308 Chirality : 0.044 0.300 4786 Planarity : 0.005 0.075 5464 Dihedral : 6.383 114.776 4299 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.86 % Favored : 92.09 % Rotamer: Outliers : 2.16 % Allowed : 15.47 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3855 helix: 0.38 (0.13), residues: 1691 sheet: -2.38 (0.23), residues: 445 loop : -2.10 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 563 HIS 0.005 0.001 HIS A 377 PHE 0.022 0.001 PHE E 557 TYR 0.028 0.001 TYR C 768 ARG 0.006 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 285 time to evaluate : 3.198 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 247 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6211 (mm-30) REVERT: A 331 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 505 TYR cc_start: 0.6006 (m-80) cc_final: 0.5114 (m-80) REVERT: B 75 MET cc_start: 0.0439 (mmm) cc_final: 0.0059 (mmm) REVERT: B 85 MET cc_start: 0.4995 (mmt) cc_final: 0.4712 (mmt) REVERT: B 754 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6726 (mt) REVERT: C 160 MET cc_start: 0.3887 (tmm) cc_final: 0.3396 (mpp) REVERT: C 262 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7548 (t) REVERT: C 496 MET cc_start: 0.7946 (mmm) cc_final: 0.7338 (mmm) REVERT: D 262 VAL cc_start: 0.7433 (t) cc_final: 0.7189 (t) REVERT: D 277 GLN cc_start: 0.6457 (pt0) cc_final: 0.6215 (mt0) REVERT: D 390 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7797 (mt) REVERT: D 426 LYS cc_start: 0.8398 (mppt) cc_final: 0.8056 (tttt) REVERT: E 258 MET cc_start: 0.3819 (tpp) cc_final: 0.3436 (tpp) outliers start: 70 outliers final: 50 residues processed: 338 average time/residue: 0.4210 time to fit residues: 237.9879 Evaluate side-chains 325 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 270 time to evaluate : 3.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 0.0980 chunk 148 optimal weight: 0.0980 chunk 221 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 235 optimal weight: 50.0000 chunk 252 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 34 optimal weight: 20.0000 chunk 291 optimal weight: 3.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31036 Z= 0.285 Angle : 0.688 10.166 42080 Z= 0.334 Chirality : 0.045 0.305 4786 Planarity : 0.005 0.078 5464 Dihedral : 6.451 115.557 4299 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.74 % Favored : 91.21 % Rotamer: Outliers : 2.59 % Allowed : 15.16 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.14), residues: 3855 helix: 0.26 (0.13), residues: 1692 sheet: -2.33 (0.24), residues: 426 loop : -2.16 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 431 HIS 0.004 0.001 HIS A 377 PHE 0.022 0.001 PHE E 557 TYR 0.028 0.002 TYR C 768 ARG 0.013 0.000 ARG B 484 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 274 time to evaluate : 3.404 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 240 GLU cc_start: 0.3663 (tt0) cc_final: 0.3264 (tm-30) REVERT: A 247 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6359 (mm-30) REVERT: A 331 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 505 TYR cc_start: 0.6208 (m-80) cc_final: 0.5125 (m-80) REVERT: B 75 MET cc_start: 0.0497 (mmm) cc_final: 0.0083 (mmm) REVERT: B 85 MET cc_start: 0.4974 (mmt) cc_final: 0.4664 (mmt) REVERT: B 754 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6800 (mt) REVERT: C 160 MET cc_start: 0.3946 (tmm) cc_final: 0.3367 (mpp) REVERT: C 262 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7584 (t) REVERT: D 217 MET cc_start: 0.6032 (tmm) cc_final: 0.5522 (ttp) REVERT: D 277 GLN cc_start: 0.6727 (pt0) cc_final: 0.6184 (mt0) REVERT: D 390 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7832 (mt) REVERT: D 426 LYS cc_start: 0.8408 (mppt) cc_final: 0.8058 (tttt) REVERT: D 698 MET cc_start: 0.5134 (ptm) cc_final: 0.4814 (ptm) REVERT: E 258 MET cc_start: 0.3952 (tpp) cc_final: 0.3550 (tpp) outliers start: 84 outliers final: 68 residues processed: 335 average time/residue: 0.3750 time to fit residues: 211.8244 Evaluate side-chains 339 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 266 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 485 MET Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.8980 chunk 355 optimal weight: 4.9990 chunk 324 optimal weight: 40.0000 chunk 345 optimal weight: 9.9990 chunk 208 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 271 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 312 optimal weight: 40.0000 chunk 327 optimal weight: 5.9990 chunk 344 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 31036 Z= 0.251 Angle : 0.670 11.438 42080 Z= 0.324 Chirality : 0.044 0.285 4786 Planarity : 0.005 0.080 5464 Dihedral : 6.377 115.070 4299 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.27 % Favored : 91.67 % Rotamer: Outliers : 2.47 % Allowed : 15.62 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.14), residues: 3855 helix: 0.32 (0.13), residues: 1689 sheet: -2.31 (0.25), residues: 419 loop : -2.16 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 507 HIS 0.004 0.001 HIS E 377 PHE 0.021 0.001 PHE E 557 TYR 0.027 0.001 TYR C 768 ARG 0.012 0.000 ARG B 484 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 276 time to evaluate : 3.588 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 247 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6322 (mm-30) REVERT: A 331 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: A 419 ILE cc_start: 0.7195 (mm) cc_final: 0.6885 (mt) REVERT: A 505 TYR cc_start: 0.6223 (m-80) cc_final: 0.5197 (m-80) REVERT: B 75 MET cc_start: 0.0485 (mmm) cc_final: 0.0050 (mmm) REVERT: B 85 MET cc_start: 0.4963 (mmt) cc_final: 0.4661 (mmt) REVERT: B 276 MET cc_start: 0.7601 (pmm) cc_final: 0.7148 (pmm) REVERT: B 754 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6817 (mt) REVERT: C 262 VAL cc_start: 0.7799 (OUTLIER) cc_final: 0.7573 (t) REVERT: D 217 MET cc_start: 0.6046 (tmm) cc_final: 0.5524 (ttp) REVERT: D 390 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7771 (mt) REVERT: D 426 LYS cc_start: 0.8359 (mppt) cc_final: 0.7995 (tttt) REVERT: D 698 MET cc_start: 0.5205 (ptm) cc_final: 0.4883 (ptm) REVERT: E 258 MET cc_start: 0.3966 (tpp) cc_final: 0.3564 (tpp) outliers start: 80 outliers final: 63 residues processed: 335 average time/residue: 0.3718 time to fit residues: 211.4628 Evaluate side-chains 336 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 268 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 528 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 707 SER Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 751 LEU Chi-restraints excluded: chain E residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.1980 chunk 365 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 173 optimal weight: 30.0000 chunk 254 optimal weight: 9.9990 chunk 383 optimal weight: 4.9990 chunk 353 optimal weight: 5.9990 chunk 305 optimal weight: 0.8980 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 20.0000 chunk 187 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 138 ASN ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 31036 Z= 0.213 Angle : 0.663 12.732 42080 Z= 0.318 Chirality : 0.044 0.267 4786 Planarity : 0.005 0.081 5464 Dihedral : 6.255 116.184 4299 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 2.19 % Allowed : 15.99 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3855 helix: 0.39 (0.13), residues: 1703 sheet: -2.28 (0.25), residues: 424 loop : -2.13 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 507 HIS 0.005 0.001 HIS E 377 PHE 0.020 0.001 PHE E 557 TYR 0.028 0.001 TYR C 768 ARG 0.011 0.000 ARG B 484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7710 Ramachandran restraints generated. 3855 Oldfield, 0 Emsley, 3855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 282 time to evaluate : 3.582 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 240 GLU cc_start: 0.3610 (tt0) cc_final: 0.3118 (tm-30) REVERT: A 247 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6312 (mm-30) REVERT: A 331 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 419 ILE cc_start: 0.7141 (mm) cc_final: 0.6820 (mt) REVERT: A 505 TYR cc_start: 0.6065 (m-80) cc_final: 0.5133 (m-80) REVERT: B 75 MET cc_start: 0.0559 (mmm) cc_final: 0.0122 (mmm) REVERT: B 85 MET cc_start: 0.4960 (mmt) cc_final: 0.4662 (mmt) REVERT: B 276 MET cc_start: 0.7568 (pmm) cc_final: 0.7170 (pmm) REVERT: B 754 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6731 (mt) REVERT: C 160 MET cc_start: 0.3860 (tmm) cc_final: 0.3335 (mmt) REVERT: C 262 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7587 (t) REVERT: D 217 MET cc_start: 0.6030 (tmm) cc_final: 0.5507 (ttp) REVERT: D 277 GLN cc_start: 0.6623 (OUTLIER) cc_final: 0.6396 (mt0) REVERT: D 390 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7739 (mt) REVERT: D 426 LYS cc_start: 0.8322 (mppt) cc_final: 0.7953 (tttt) REVERT: D 440 LEU cc_start: 0.7694 (mt) cc_final: 0.7364 (mt) REVERT: E 75 MET cc_start: 0.1724 (ptp) cc_final: 0.1454 (ptp) REVERT: E 258 MET cc_start: 0.4026 (tpp) cc_final: 0.3633 (tpp) outliers start: 71 outliers final: 58 residues processed: 334 average time/residue: 0.3784 time to fit residues: 213.5115 Evaluate side-chains 341 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 211 GLN Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 662 ASP Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 ASP Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 494 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain E residue 715 ILE Chi-restraints excluded: chain E residue 751 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 93 optimal weight: 50.0000 chunk 281 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 50.0000 chunk 305 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.210921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.153207 restraints weight = 62375.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.151539 restraints weight = 41430.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.151335 restraints weight = 28956.855| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31036 Z= 0.279 Angle : 0.695 11.910 42080 Z= 0.335 Chirality : 0.045 0.268 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.320 117.791 4299 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.90 % Favored : 91.05 % Rotamer: Outliers : 2.25 % Allowed : 16.02 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.91 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3855 helix: 0.31 (0.13), residues: 1700 sheet: -2.21 (0.26), residues: 410 loop : -2.14 (0.15), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 507 HIS 0.004 0.001 HIS A 319 PHE 0.021 0.001 PHE E 557 TYR 0.030 0.002 TYR C 768 ARG 0.011 0.000 ARG B 484 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6246.01 seconds wall clock time: 115 minutes 3.50 seconds (6903.50 seconds total)