Starting phenix.real_space_refine on Wed Feb 21 11:30:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/02_2024/7yuw_34113_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/02_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_34113/02_2024/7yuw_34113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/02_2024/7yuw_34113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/02_2024/7yuw_34113_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuw_34113/02_2024/7yuw_34113_updated.pdb" } 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.16, per 1000 atoms: 0.53 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: 10.95 Conformation dependent library (CDL) restraints added in 5.4 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... running ksdssp... Secondary structure from input PDB file: 140 helices and 36 sheets defined 39.6% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.818A pdb=" N VAL A 34 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 234 removed outlier: 3.736A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 309 through 319 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) Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 445 through 448 No H-bonds generated for 'chain 'A' and resid 445 through 448' Processing helix chain 'A' and resid 479 through 482 No H-bonds generated for 'chain 'A' and resid 479 through 482' Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 507 through 514 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 559 Processing helix chain 'A' and resid 574 through 577 No H-bonds generated for 'chain 'A' and resid 574 through 577' Processing helix chain 'A' and resid 631 through 644 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 741 through 745 Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 762 through 769 Processing helix chain 'B' and resid 31 through 39 removed outlier: 4.384A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 118 through 138 removed outlier: 3.894A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 158 through 168 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 173 through 180 removed outlier: 3.866A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 236 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 240 through 244 Processing helix chain 'B' and resid 248 through 254 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 311 through 317 Processing helix chain 'B' and resid 325 through 337 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 435 through 442 removed outlier: 4.017A pdb=" N GLU B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 448 No H-bonds generated for 'chain 'B' and resid 445 through 448' Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 495 through 505 removed outlier: 3.842A pdb=" N ALA B 500 " --> pdb=" O MET B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 631 through 650 removed outlier: 3.992A pdb=" N THR B 648 " --> pdb=" O ARG B 645 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 649 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 727 Processing helix chain 'B' and resid 737 through 745 removed outlier: 3.961A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU B 745 " --> pdb=" O GLN B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 4.292A pdb=" N LEU B 766 " --> pdb=" O GLY B 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 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 119 through 137 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 146 through 151 Processing helix chain 'C' and resid 158 through 168 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 173 through 181 Processing helix chain 'C' and resid 185 through 235 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 260 through 271 Processing helix chain 'C' and resid 281 through 295 removed outlier: 4.069A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 361 through 370 Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 435 through 443 removed outlier: 3.539A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 482 No H-bonds generated for 'chain 'C' and resid 479 through 482' Processing helix chain 'C' and resid 495 through 502 Processing helix chain 'C' and resid 507 through 513 Processing helix chain 'C' and resid 524 through 534 Processing helix chain 'C' and resid 542 through 559 Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 726 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.824A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 Processing helix chain 'D' and resid 31 through 39 removed outlier: 3.720A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 removed outlier: 3.536A pdb=" N ASN D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 154 removed outlier: 3.537A pdb=" N GLY D 154 " --> pdb=" O ALA D 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 151 through 154' Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 180 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 185 through 237 Processing helix chain 'D' and resid 246 through 255 Processing helix chain 'D' and resid 260 through 271 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 308 through 317 removed outlier: 3.519A pdb=" N ASP D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 337 removed outlier: 3.514A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.140A pdb=" N ARG D 366 " --> pdb=" O THR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 436 through 443 Processing helix chain 'D' and resid 474 through 476 No H-bonds generated for 'chain 'D' and resid 474 through 476' Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 507 through 513 removed outlier: 3.984A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.536A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 578 Processing helix chain 'D' and resid 587 through 589 No H-bonds generated for 'chain 'D' and resid 587 through 589' Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 723 Processing helix chain 'D' and resid 737 through 739 No H-bonds generated for 'chain 'D' and resid 737 through 739' Processing helix chain 'D' and resid 741 through 743 No H-bonds generated for 'chain 'D' and resid 741 through 743' Processing helix chain 'D' and resid 765 through 769 removed outlier: 3.652A pdb=" N LEU D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 765 through 769' Processing helix chain 'E' and resid 31 through 39 Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 118 through 138 Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 185 through 232 removed outlier: 4.122A pdb=" N LEU E 189 " --> pdb=" O LEU E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 242 Processing helix chain 'E' and resid 248 through 255 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 260 through 271 Processing helix chain 'E' and resid 281 through 294 Processing helix chain 'E' and resid 308 through 317 removed outlier: 4.364A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.909A pdb=" N GLY E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 Processing helix chain 'E' and resid 424 through 426 No H-bonds generated for 'chain 'E' and resid 424 through 426' Processing helix chain 'E' and resid 435 through 443 removed outlier: 3.605A pdb=" N LEU E 443 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 445 through 448 No H-bonds generated for 'chain 'E' and resid 445 through 448' Processing helix chain 'E' and resid 479 through 481 No H-bonds generated for 'chain 'E' and resid 479 through 481' Processing helix chain 'E' and resid 495 through 513 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 524 through 534 Processing helix chain 'E' and resid 541 through 559 Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 631 through 646 Processing helix chain 'E' and resid 648 through 650 No H-bonds generated for 'chain 'E' and resid 648 through 650' Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 680 through 690 Processing helix chain 'E' and resid 718 through 727 Processing helix chain 'E' and resid 737 through 739 No H-bonds generated for 'chain 'E' and resid 737 through 739' Processing helix chain 'E' and resid 763 through 769 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 removed outlier: 6.134A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL A 71 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 Processing sheet with id= C, first strand: chain 'A' and resid 377 through 380 removed outlier: 3.510A pdb=" N HIS A 377 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 379 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.913A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, 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= F, first strand: chain 'A' and resid 732 through 736 removed outlier: 6.314A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N LYS A 757 " --> pdb=" O LEU A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.707A pdb=" N GLN B 73 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 43 through 45 removed outlier: 4.114A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B 88 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 352 through 355 Processing sheet with id= J, first strand: chain 'B' and resid 376 through 378 removed outlier: 6.708A pdb=" N VAL B 418 " --> pdb=" O HIS B 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, 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= L, first strand: chain 'B' and resid 700 through 702 removed outlier: 6.677A pdb=" N LYS B 732 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 20 through 23 removed outlier: 4.284A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 469 through 471 removed outlier: 3.674A pdb=" N VAL C 354 " --> pdb=" O ILE C 488 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.450A pdb=" N VAL C 418 " --> pdb=" O HIS C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.313A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, 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) Processing sheet with id= R, first strand: chain 'C' and resid 613 through 615 removed outlier: 6.131A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id= S, 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= T, 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= U, 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: 4.251A pdb=" N THR D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 77 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN D 83 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 43 through 46 removed outlier: 3.553A pdb=" N GLY D 66 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 418 through 420 removed outlier: 6.934A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 520 through 522 removed outlier: 5.954A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, 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: 7.090A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id= Z, 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= AA, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.378A pdb=" N LYS D 732 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'D' and resid 705 through 707 Processing sheet with id= AC, 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= AD, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.888A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 70 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 352 through 355 Processing sheet with id= AF, first strand: chain 'E' and resid 376 through 380 removed outlier: 6.222A pdb=" N VAL E 418 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE E 379 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 420 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N LEU E 421 " --> pdb=" O PHE E 466 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE E 468 " --> pdb=" O LEU E 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.385A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, 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) removed outlier: 3.785A pdb=" N VAL E 667 " --> pdb=" O THR E 626 " (cutoff:3.500A) Processing sheet with id= AI, 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) Processing sheet with id= AJ, first strand: chain 'E' and resid 732 through 736 removed outlier: 6.148A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ 1078 hydrogen bonds defined for protein. 3063 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: 10.01 Time building geometry restraints manager: 11.95 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: 801 2.69 - 3.25: 30741 3.25 - 3.80: 47955 3.80 - 4.35: 63515 4.35 - 4.90: 102510 Nonbonded interactions: 245522 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 245517 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.820 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 76.700 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.120 ------------------------------------------------------------------------------- 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= 0.250 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 : 3.237 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: 0.3675 time to fit residues: 215.9067 Evaluate side-chains 269 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 268 time to evaluate : 3.249 ------------------------------------------------------------------------------- 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: 30.0000 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 196 optimal weight: 0.0470 chunk 155 optimal weight: 20.0000 chunk 301 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 183 optimal weight: 9.9990 chunk 224 optimal weight: 0.6980 chunk 349 optimal weight: 4.9990 overall best weight: 3.1484 ------------------------------------------------------------------------------- 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** A 510 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 HIS ** C 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 739 ASN E 234 GLN E 495 ASN E 666 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 31036 Z= 0.308 Angle : 0.696 8.773 42080 Z= 0.344 Chirality : 0.046 0.279 4786 Planarity : 0.005 0.065 5464 Dihedral : 7.607 175.548 4301 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.26 % Favored : 90.66 % Rotamer: Outliers : 1.05 % Allowed : 7.43 % Favored : 91.53 % 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: -2.12 (0.13), residues: 3855 helix: -0.10 (0.13), residues: 1661 sheet: -2.60 (0.23), residues: 440 loop : -2.39 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 292 HIS 0.006 0.001 HIS C 454 PHE 0.021 0.002 PHE C 657 TYR 0.038 0.002 TYR C 768 ARG 0.005 0.000 ARG D 222 *********************** 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 316 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 282 time to evaluate : 3.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3481 (p90) cc_final: 0.2840 (p90) REVERT: B 85 MET cc_start: 0.4864 (mmt) cc_final: 0.4475 (mmt) REVERT: B 488 ILE cc_start: 0.8093 (mm) cc_final: 0.7549 (mt) REVERT: C 160 MET cc_start: 0.3745 (tmm) cc_final: 0.3390 (mpp) REVERT: C 230 MET cc_start: 0.7676 (tmm) cc_final: 0.7288 (tmm) REVERT: C 258 MET cc_start: 0.5076 (ttm) cc_final: 0.4682 (ttm) REVERT: C 625 LEU cc_start: 0.8011 (mt) cc_final: 0.7759 (mt) REVERT: E 85 MET cc_start: 0.5463 (mpp) cc_final: 0.4310 (mpp) REVERT: E 258 MET cc_start: 0.4560 (tpp) cc_final: 0.4273 (tpp) REVERT: E 635 GLU cc_start: 0.7867 (pm20) cc_final: 0.7414 (pm20) outliers start: 34 outliers final: 24 residues processed: 299 average time/residue: 0.3876 time to fit residues: 194.8492 Evaluate side-chains 281 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 257 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU 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 608 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 290 LEU 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 612 ILE Chi-restraints excluded: chain D residue 681 ILE 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: 3.9990 chunk 108 optimal weight: 0.4980 chunk 290 optimal weight: 2.9990 chunk 238 optimal weight: 30.0000 chunk 96 optimal weight: 40.0000 chunk 350 optimal weight: 20.0000 chunk 378 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 347 optimal weight: 50.0000 chunk 119 optimal weight: 5.9990 chunk 280 optimal weight: 0.5980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31036 Z= 0.281 Angle : 0.670 8.874 42080 Z= 0.330 Chirality : 0.045 0.288 4786 Planarity : 0.005 0.062 5464 Dihedral : 7.465 166.345 4301 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 1.85 % Allowed : 9.92 % Favored : 88.23 % 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: -2.05 (0.13), residues: 3855 helix: -0.02 (0.13), residues: 1642 sheet: -2.49 (0.23), residues: 439 loop : -2.38 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 292 HIS 0.004 0.001 HIS C 454 PHE 0.014 0.001 PHE C 657 TYR 0.034 0.002 TYR C 768 ARG 0.005 0.000 ARG E 91 *********************** 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 341 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 281 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3479 (p90) cc_final: 0.2902 (p90) REVERT: A 507 TRP cc_start: 0.5858 (t60) cc_final: 0.5586 (t60) REVERT: B 85 MET cc_start: 0.4970 (mmt) cc_final: 0.4628 (mmt) REVERT: B 230 MET cc_start: 0.3163 (mtt) cc_final: 0.2640 (mmp) REVERT: C 160 MET cc_start: 0.3615 (tmm) cc_final: 0.3259 (mmm) REVERT: C 625 LEU cc_start: 0.8006 (mt) cc_final: 0.7782 (mt) REVERT: D 229 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6531 (tt0) REVERT: E 85 MET cc_start: 0.5414 (mpp) cc_final: 0.4362 (mpp) REVERT: E 258 MET cc_start: 0.4494 (tpp) cc_final: 0.4244 (tpp) REVERT: E 631 GLU cc_start: 0.6550 (tp30) cc_final: 0.5980 (tp30) outliers start: 60 outliers final: 42 residues processed: 315 average time/residue: 0.3811 time to fit residues: 202.1995 Evaluate side-chains 301 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 259 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU 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 617 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 681 ILE 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 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 703 THR Chi-restraints excluded: chain C residue 769 LEU 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 372 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 414 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 3.9990 chunk 263 optimal weight: 0.5980 chunk 181 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 235 optimal weight: 50.0000 chunk 351 optimal weight: 30.0000 chunk 372 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 333 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 GLN ** 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** E 168 HIS E 177 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.1640 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= 0.404 Angle : 0.755 10.521 42080 Z= 0.372 Chirality : 0.047 0.296 4786 Planarity : 0.006 0.069 5464 Dihedral : 7.585 156.647 4299 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.35 % Favored : 89.57 % Rotamer: Outliers : 2.80 % Allowed : 12.23 % Favored : 84.96 % 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: -2.23 (0.13), residues: 3855 helix: -0.23 (0.13), residues: 1640 sheet: -2.43 (0.24), residues: 414 loop : -2.46 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 298 HIS 0.007 0.001 HIS C 454 PHE 0.018 0.002 PHE A 376 TYR 0.027 0.002 TYR C 768 ARG 0.005 0.000 ARG A 378 *********************** 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 372 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 281 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3511 (p90) cc_final: 0.2901 (p90) REVERT: A 247 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6450 (mm-30) REVERT: B 85 MET cc_start: 0.4832 (mmt) cc_final: 0.4487 (mmt) REVERT: B 230 MET cc_start: 0.3125 (mtt) cc_final: 0.2920 (mmp) REVERT: B 496 MET cc_start: 0.8025 (tpp) cc_final: 0.7821 (tpp) REVERT: B 635 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: B 754 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.6925 (mp) REVERT: C 160 MET cc_start: 0.3704 (tmm) cc_final: 0.3348 (mpp) REVERT: C 439 MET cc_start: 0.7597 (mmm) cc_final: 0.7350 (mmm) REVERT: C 625 LEU cc_start: 0.8160 (mt) cc_final: 0.7929 (mt) REVERT: D 229 GLN cc_start: 0.6996 (tp-100) cc_final: 0.6584 (tt0) REVERT: D 277 GLN cc_start: 0.6526 (pt0) cc_final: 0.6187 (mt0) REVERT: D 631 GLU cc_start: 0.6584 (tp30) cc_final: 0.6132 (tp30) REVERT: D 635 GLU cc_start: 0.6040 (mm-30) cc_final: 0.5725 (mm-30) REVERT: E 85 MET cc_start: 0.5198 (mpp) cc_final: 0.4473 (mpp) REVERT: E 258 MET cc_start: 0.4612 (tpp) cc_final: 0.4386 (tpp) REVERT: E 265 LYS cc_start: 0.4142 (pttt) cc_final: 0.3239 (tttp) REVERT: E 713 MET cc_start: 0.7351 (ttp) cc_final: 0.7086 (mtm) outliers start: 91 outliers final: 65 residues processed: 342 average time/residue: 0.3881 time to fit residues: 222.6532 Evaluate side-chains 333 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 265 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 314 VAL 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 443 LEU 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 617 VAL Chi-restraints excluded: chain B residue 635 GLU Chi-restraints excluded: chain B residue 645 ARG 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 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 470 THR 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 681 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 715 ILE Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 LEU 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 372 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 412 VAL 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 450 THR Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 568 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 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 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 488 ILE 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 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: 0.9980 chunk 153 optimal weight: 0.9990 chunk 317 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 0.6980 chunk 334 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 319 HIS ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 31036 Z= 0.279 Angle : 0.681 8.966 42080 Z= 0.334 Chirality : 0.045 0.304 4786 Planarity : 0.005 0.071 5464 Dihedral : 7.306 149.994 4299 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.72 % Favored : 91.21 % Rotamer: Outliers : 2.65 % Allowed : 14.02 % Favored : 83.33 % 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: -2.08 (0.13), residues: 3855 helix: -0.08 (0.13), residues: 1646 sheet: -2.51 (0.23), residues: 437 loop : -2.36 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 602 HIS 0.005 0.001 HIS E 377 PHE 0.012 0.001 PHE C 466 TYR 0.026 0.002 TYR C 768 ARG 0.005 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 363 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 277 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3497 (p90) cc_final: 0.2897 (p90) REVERT: A 247 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6449 (mm-30) REVERT: A 419 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7012 (mt) REVERT: A 507 TRP cc_start: 0.6021 (t60) cc_final: 0.5740 (t60) REVERT: B 85 MET cc_start: 0.4963 (mmt) cc_final: 0.4653 (mmt) REVERT: B 230 MET cc_start: 0.3234 (mtt) cc_final: 0.2816 (mmp) REVERT: B 598 GLN cc_start: 0.7048 (mt0) cc_final: 0.6818 (mt0) REVERT: B 635 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: B 754 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6872 (mt) REVERT: C 160 MET cc_start: 0.3635 (tmm) cc_final: 0.3314 (mpp) REVERT: D 229 GLN cc_start: 0.6789 (tp-100) cc_final: 0.6516 (tt0) REVERT: D 277 GLN cc_start: 0.6475 (pt0) cc_final: 0.6138 (mt0) REVERT: E 85 MET cc_start: 0.5254 (mpp) cc_final: 0.4221 (mpp) REVERT: E 258 MET cc_start: 0.4580 (tpp) cc_final: 0.4307 (tpp) REVERT: E 713 MET cc_start: 0.7278 (ttp) cc_final: 0.7052 (mtm) outliers start: 86 outliers final: 56 residues processed: 338 average time/residue: 0.3648 time to fit residues: 209.2401 Evaluate side-chains 324 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 264 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL 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 419 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 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 470 THR 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 635 GLU Chi-restraints excluded: chain B residue 645 ARG 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 769 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 470 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 570 ASP Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 414 VAL 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 511 VAL 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 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 465 VAL 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 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 1.9990 chunk 335 optimal weight: 40.0000 chunk 73 optimal weight: 9.9990 chunk 218 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 372 optimal weight: 20.0000 chunk 309 optimal weight: 40.0000 chunk 172 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 HIS ** 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 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31036 Z= 0.198 Angle : 0.628 8.919 42080 Z= 0.306 Chirality : 0.043 0.314 4786 Planarity : 0.005 0.073 5464 Dihedral : 6.774 125.704 4299 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.07 % Favored : 91.85 % Rotamer: Outliers : 2.47 % Allowed : 14.73 % Favored : 82.80 % 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: -1.81 (0.14), residues: 3855 helix: 0.21 (0.13), residues: 1650 sheet: -2.49 (0.23), residues: 456 loop : -2.25 (0.15), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 292 HIS 0.005 0.001 HIS E 377 PHE 0.009 0.001 PHE B 376 TYR 0.025 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 370 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 290 time to evaluate : 3.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3606 (p90) cc_final: 0.2983 (p90) REVERT: A 247 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6416 (mm-30) REVERT: B 85 MET cc_start: 0.4961 (mmt) cc_final: 0.4646 (mmt) REVERT: B 635 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: B 754 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6819 (mt) REVERT: C 160 MET cc_start: 0.3585 (tmm) cc_final: 0.3354 (mpp) REVERT: C 230 MET cc_start: 0.7678 (tmm) cc_final: 0.7438 (tmm) REVERT: C 353 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7203 (mp) REVERT: C 378 ARG cc_start: 0.8335 (tmm-80) cc_final: 0.7861 (ttt-90) REVERT: C 469 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8716 (t) REVERT: D 277 GLN cc_start: 0.6386 (pt0) cc_final: 0.6027 (mt0) REVERT: D 390 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7771 (mt) REVERT: E 85 MET cc_start: 0.5050 (mpp) cc_final: 0.4617 (mpp) REVERT: E 258 MET cc_start: 0.4514 (tpp) cc_final: 0.4267 (tpp) outliers start: 80 outliers final: 54 residues processed: 348 average time/residue: 0.3602 time to fit residues: 212.8824 Evaluate side-chains 326 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 266 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU 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 514 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU 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 635 GLU Chi-restraints excluded: chain B residue 645 ARG 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 769 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 470 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 516 MET 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 768 TYR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 335 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 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 681 ILE Chi-restraints excluded: chain D residue 703 THR 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 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 664 HIS Chi-restraints excluded: chain E residue 681 ILE 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: 1.9990 chunk 41 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 313 optimal weight: 40.0000 chunk 208 optimal weight: 3.9990 chunk 371 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 229 GLN ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 31036 Z= 0.323 Angle : 0.710 12.116 42080 Z= 0.344 Chirality : 0.046 0.424 4786 Planarity : 0.005 0.077 5464 Dihedral : 6.810 110.329 4299 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.52 % Favored : 90.40 % Rotamer: Outliers : 3.14 % Allowed : 15.38 % Favored : 81.48 % 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: -1.95 (0.14), residues: 3855 helix: 0.03 (0.13), residues: 1654 sheet: -2.50 (0.24), residues: 438 loop : -2.28 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 602 HIS 0.005 0.001 HIS E 731 PHE 0.021 0.002 PHE E 557 TYR 0.024 0.002 TYR C 768 ARG 0.004 0.000 ARG C 345 *********************** 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 370 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 268 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3646 (p90) cc_final: 0.2985 (p90) REVERT: A 247 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6520 (mm-30) REVERT: B 85 MET cc_start: 0.4895 (mmt) cc_final: 0.4603 (mmt) REVERT: B 754 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6857 (mt) REVERT: C 38 MET cc_start: -0.1560 (mtm) cc_final: -0.2058 (mtp) REVERT: C 160 MET cc_start: 0.3474 (tmm) cc_final: 0.3134 (mpp) REVERT: C 230 MET cc_start: 0.7682 (tmm) cc_final: 0.7446 (tmm) REVERT: C 726 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6698 (t-90) REVERT: D 217 MET cc_start: 0.5901 (tmm) cc_final: 0.5433 (ttp) REVERT: D 516 MET cc_start: 0.7967 (mmm) cc_final: 0.7684 (mmm) REVERT: E 85 MET cc_start: 0.5162 (mpp) cc_final: 0.4582 (mpp) REVERT: E 258 MET cc_start: 0.4664 (tpp) cc_final: 0.4420 (tpp) REVERT: E 265 LYS cc_start: 0.4229 (pttt) cc_final: 0.3268 (mmmt) outliers start: 102 outliers final: 71 residues processed: 341 average time/residue: 0.4148 time to fit residues: 241.5087 Evaluate side-chains 333 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 259 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU 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 514 SER 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 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ARG 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 769 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 470 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 570 ASP Chi-restraints excluded: chain C residue 594 VAL 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 703 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 LEU 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 372 MET Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 412 VAL 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 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 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 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 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 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: 0.9980 chunk 148 optimal weight: 0.0870 chunk 221 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 235 optimal weight: 50.0000 chunk 252 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 291 optimal weight: 4.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31036 Z= 0.212 Angle : 0.656 11.367 42080 Z= 0.316 Chirality : 0.044 0.375 4786 Planarity : 0.005 0.079 5464 Dihedral : 6.515 111.359 4299 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.70 % Favored : 92.22 % Rotamer: Outliers : 2.53 % Allowed : 16.21 % Favored : 81.26 % 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: -1.77 (0.14), residues: 3855 helix: 0.22 (0.13), residues: 1651 sheet: -2.44 (0.24), residues: 437 loop : -2.21 (0.15), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 507 HIS 0.005 0.001 HIS E 377 PHE 0.013 0.001 PHE E 557 TYR 0.024 0.001 TYR C 768 ARG 0.010 0.000 ARG A 378 *********************** 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 362 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 280 time to evaluate : 3.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3665 (p90) cc_final: 0.3026 (p90) REVERT: A 247 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6426 (mm-30) REVERT: B 85 MET cc_start: 0.4882 (mmt) cc_final: 0.4598 (mmt) REVERT: B 754 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6808 (mt) REVERT: C 160 MET cc_start: 0.3463 (tmm) cc_final: 0.3174 (mpp) REVERT: C 258 MET cc_start: 0.4766 (ttm) cc_final: 0.4430 (ttm) REVERT: C 378 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.7851 (ttt-90) REVERT: D 217 MET cc_start: 0.5873 (tmm) cc_final: 0.5403 (ttp) REVERT: D 277 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.6071 (mt0) REVERT: E 85 MET cc_start: 0.5096 (mpp) cc_final: 0.4544 (mpp) REVERT: E 258 MET cc_start: 0.4595 (tpp) cc_final: 0.4368 (tpp) outliers start: 82 outliers final: 66 residues processed: 340 average time/residue: 0.3598 time to fit residues: 209.2298 Evaluate side-chains 334 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 265 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU 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 456 LEU Chi-restraints excluded: chain A residue 514 SER 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 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ARG 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 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 470 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 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 703 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 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 386 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 414 VAL 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 641 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR 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 315 LEU Chi-restraints excluded: chain E residue 431 TRP Chi-restraints excluded: chain E residue 465 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 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: 9.9990 chunk 355 optimal weight: 20.0000 chunk 324 optimal weight: 40.0000 chunk 345 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 271 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 312 optimal weight: 0.8980 chunk 327 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** D 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 31036 Z= 0.322 Angle : 0.719 11.897 42080 Z= 0.348 Chirality : 0.046 0.342 4786 Planarity : 0.005 0.081 5464 Dihedral : 6.644 111.430 4299 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.70 % Favored : 90.25 % Rotamer: Outliers : 2.71 % Allowed : 16.61 % Favored : 80.68 % 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: 0.01 (0.13), residues: 1650 sheet: -2.42 (0.25), residues: 410 loop : -2.24 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 507 HIS 0.005 0.001 HIS A 319 PHE 0.026 0.002 PHE E 557 TYR 0.025 0.002 TYR C 768 ARG 0.008 0.000 ARG A 378 *********************** 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: 88 poor density : 268 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3643 (p90) cc_final: 0.2986 (p90) REVERT: A 247 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6506 (mm-30) REVERT: A 698 MET cc_start: 0.3418 (mmt) cc_final: 0.3183 (mmt) REVERT: B 85 MET cc_start: 0.4905 (mmt) cc_final: 0.4623 (mmt) REVERT: B 754 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6843 (mt) REVERT: C 160 MET cc_start: 0.3510 (tmm) cc_final: 0.3136 (mpp) REVERT: C 482 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8041 (tt) REVERT: D 217 MET cc_start: 0.5865 (tmm) cc_final: 0.5423 (ttp) REVERT: D 277 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.6089 (mt0) REVERT: D 768 TYR cc_start: 0.6827 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: E 85 MET cc_start: 0.5106 (mpp) cc_final: 0.4567 (mpp) REVERT: E 258 MET cc_start: 0.4682 (tpp) cc_final: 0.4452 (tpp) REVERT: E 265 LYS cc_start: 0.4253 (pttt) cc_final: 0.3313 (mmmt) REVERT: E 485 MET cc_start: 0.5563 (tpp) cc_final: 0.5197 (tmm) outliers start: 88 outliers final: 71 residues processed: 333 average time/residue: 0.3526 time to fit residues: 200.8784 Evaluate side-chains 340 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 264 time to evaluate : 3.507 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain A residue 514 SER 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 364 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 608 THR Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 645 ARG 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 325 VAL Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 594 VAL 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 703 THR Chi-restraints excluded: chain C residue 723 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 ASP Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 414 VAL 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 608 THR Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 703 THR Chi-restraints excluded: chain D residue 722 LEU Chi-restraints excluded: chain D residue 749 GLU Chi-restraints excluded: chain D residue 768 TYR Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 84 VAL 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 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 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: 0.0770 chunk 365 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 173 optimal weight: 30.0000 chunk 254 optimal weight: 10.0000 chunk 383 optimal weight: 3.9990 chunk 353 optimal weight: 0.9980 chunk 305 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 235 optimal weight: 50.0000 chunk 187 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 HIS ** 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 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 HIS ** 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: 0.6329 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31036 Z= 0.176 Angle : 0.649 13.188 42080 Z= 0.311 Chirality : 0.044 0.369 4786 Planarity : 0.005 0.080 5464 Dihedral : 6.259 112.896 4299 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.72 % Favored : 93.23 % Rotamer: Outliers : 1.69 % Allowed : 17.57 % Favored : 80.74 % 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: -1.65 (0.14), residues: 3855 helix: 0.31 (0.13), residues: 1649 sheet: -2.44 (0.24), residues: 441 loop : -2.12 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 507 HIS 0.005 0.001 HIS E 377 PHE 0.026 0.001 PHE E 557 TYR 0.028 0.001 TYR D 225 ARG 0.009 0.000 ARG A 378 ********************** 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 347 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.3728 (p90) cc_final: 0.3081 (p90) REVERT: A 247 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6346 (mm-30) REVERT: A 419 ILE cc_start: 0.7073 (mm) cc_final: 0.6851 (mt) REVERT: A 505 TYR cc_start: 0.6129 (m-80) cc_final: 0.5216 (m-80) REVERT: B 85 MET cc_start: 0.4890 (mmt) cc_final: 0.4602 (mmt) REVERT: B 754 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6734 (mt) REVERT: C 160 MET cc_start: 0.3496 (tmm) cc_final: 0.3250 (mpp) REVERT: C 378 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.7887 (ttt-90) REVERT: D 217 MET cc_start: 0.6045 (tmm) cc_final: 0.5515 (ttp) REVERT: D 440 LEU cc_start: 0.7687 (mt) cc_final: 0.7432 (mt) REVERT: E 85 MET cc_start: 0.5083 (mpp) cc_final: 0.4609 (mpp) REVERT: E 485 MET cc_start: 0.5527 (tpp) cc_final: 0.5009 (tmm) outliers start: 55 outliers final: 44 residues processed: 330 average time/residue: 0.3819 time to fit residues: 213.7306 Evaluate side-chains 319 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 273 time to evaluate : 3.361 ------------------------------------------------------------------------------- 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 456 LEU Chi-restraints excluded: chain B residue 45 PHE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 386 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 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 412 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 570 ASP Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 698 MET Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 769 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 414 VAL 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 703 THR 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 431 TRP Chi-restraints excluded: chain E residue 465 VAL Chi-restraints excluded: chain E residue 681 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 242 optimal weight: 30.0000 chunk 325 optimal weight: 20.0000 chunk 93 optimal weight: 40.0000 chunk 281 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 84 optimal weight: 40.0000 chunk 305 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 314 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 313 GLN ** C 168 HIS ** 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 664 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.203761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.146586 restraints weight = 60321.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.143012 restraints weight = 42779.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143239 restraints weight = 33019.817| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.140 31036 Z= 0.590 Angle : 0.918 14.181 42080 Z= 0.451 Chirality : 0.053 0.310 4786 Planarity : 0.007 0.080 5464 Dihedral : 7.050 108.593 4299 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.23 % Favored : 88.72 % Rotamer: Outliers : 2.53 % Allowed : 17.44 % Favored : 80.03 % 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: -2.38 (0.13), residues: 3855 helix: -0.43 (0.13), residues: 1639 sheet: -2.64 (0.24), residues: 428 loop : -2.41 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 507 HIS 0.015 0.002 HIS C 726 PHE 0.026 0.003 PHE E 557 TYR 0.027 0.003 TYR D 643 ARG 0.009 0.001 ARG C 345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6077.48 seconds wall clock time: 112 minutes 2.41 seconds (6722.41 seconds total)