Starting phenix.real_space_refine on Thu Mar 21 15:45:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypj_34002/03_2024/7ypj_34002_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 5780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A GLU 740": "OE1" <-> "OE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 282": "OE1" <-> "OE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "D GLU 423": "OE1" <-> "OE2" Residue "D GLU 613": "OE1" <-> "OE2" Residue "D GLU 745": "OE1" <-> "OE2" Residue "D GLU 773": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Residue "E GLU 255": "OE1" <-> "OE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 304": "OE1" <-> "OE2" Residue "E GLU 517": "OE1" <-> "OE2" Residue "E GLU 631": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30478 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6074 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: 15.63, per 1000 atoms: 0.51 Number of scatterers: 30478 At special positions: 0 Unit cell: (168.699, 169.76, 188.858, 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 5780 8.00 N 5355 7.00 C 19230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 7.5 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: 145 helices and 30 sheets defined 41.3% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.15 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.706A pdb=" N VAL A 34 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 removed outlier: 3.548A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) 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 235 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 281 through 295 removed outlier: 5.017A pdb=" N ALA A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.553A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.548A pdb=" N ILE A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 404 through 410 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 504 Processing helix chain 'A' and resid 506 through 512 Processing helix chain 'A' and resid 524 through 533 Processing helix chain 'A' and resid 541 through 559 Processing helix chain 'A' and resid 572 through 577 Proline residue: A 575 - end of helix No H-bonds generated for 'chain 'A' and resid 572 through 577' Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 657 through 660 No H-bonds generated for 'chain 'A' and resid 657 through 660' Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 727 Processing helix chain 'A' and resid 741 through 745 removed outlier: 3.879A pdb=" N GLU A 745 " --> pdb=" O GLN A 742 " (cutoff:3.500A) 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: 4.559A 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: 3.996A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.612A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 165 Processing helix chain 'B' and resid 173 through 180 Processing helix chain 'B' and resid 187 through 236 Processing helix chain 'B' and resid 240 through 255 removed outlier: 6.359A pdb=" N LEU B 246 " --> pdb=" O GLY B 242 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.986A pdb=" N LEU B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 295 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.732A pdb=" N HIS B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) 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 410 Processing helix chain 'B' and resid 436 through 443 removed outlier: 4.565A pdb=" N VAL B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 443 " --> pdb=" O MET B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 449 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 Processing helix chain 'B' and resid 507 through 513 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 559 Processing helix chain 'B' and resid 574 through 577 No H-bonds generated for 'chain 'B' and resid 574 through 577' Processing helix chain 'B' and resid 631 through 645 Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 718 through 726 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.985A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'C' and resid 30 through 38 removed outlier: 5.045A pdb=" N GLU C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 138 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 153 Processing helix chain 'C' and resid 158 through 168 removed outlier: 4.172A pdb=" N ALA C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 4.454A 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 237 removed outlier: 3.732A pdb=" N GLU C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 237 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 255 removed outlier: 3.718A pdb=" N SER C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 309 through 318 Processing helix chain 'C' and resid 325 through 338 Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 436 through 443 Processing helix chain 'C' and resid 447 through 450 removed outlier: 3.928A pdb=" N THR C 450 " --> pdb=" O GLN C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 447 through 450' 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 496 through 504 Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.527A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 533 removed outlier: 3.699A pdb=" N LEU C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 559 Processing helix chain 'C' and resid 574 through 577 No H-bonds generated for 'chain 'C' and resid 574 through 577' Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 680 through 691 Processing helix chain 'C' and resid 718 through 726 Processing helix chain 'C' and resid 737 through 744 removed outlier: 3.819A pdb=" N ALA C 741 " --> pdb=" O LYS C 737 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN C 742 " --> pdb=" O ASP C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 750 No H-bonds generated for 'chain 'C' and resid 748 through 750' Processing helix chain 'C' and resid 762 through 773 removed outlier: 4.536A pdb=" N LEU C 771 " --> pdb=" O GLU C 767 " (cutoff:3.500A) Proline residue: C 772 - end of helix Processing helix chain 'D' and resid 31 through 39 removed outlier: 3.809A pdb=" N GLY D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 138 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 158 through 168 Processing helix chain 'D' and resid 173 through 180 Processing helix chain 'D' and resid 185 through 237 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 245 through 255 removed outlier: 4.348A pdb=" N ARG D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 272 Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 326 through 337 removed outlier: 3.636A pdb=" N ARG D 336 " --> pdb=" O TYR D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 Processing helix chain 'D' and resid 387 through 390 No H-bonds generated for 'chain 'D' and resid 387 through 390' Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 436 through 443 Processing helix chain 'D' and resid 447 through 450 removed outlier: 4.064A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 447 through 450' 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 505 Processing helix chain 'D' and resid 507 through 513 Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 541 through 559 removed outlier: 3.905A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 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 634 through 645 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 691 Processing helix chain 'D' and resid 718 through 728 removed outlier: 3.747A pdb=" N HIS D 726 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.748A pdb=" N LEU D 743 " --> pdb=" O GLU D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 748 through 751 No H-bonds generated for 'chain 'D' and resid 748 through 751' Processing helix chain 'E' and resid 28 through 38 removed outlier: 4.310A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) 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 168 Processing helix chain 'E' and resid 173 through 181 Processing helix chain 'E' and resid 185 through 244 removed outlier: 4.137A pdb=" N GLU E 236 " --> pdb=" O ALA E 232 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU E 237 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.577A pdb=" N VAL E 285 " --> pdb=" O GLU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 294 No H-bonds generated for 'chain 'E' and resid 291 through 294' Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.932A pdb=" N GLU E 317 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 361 through 371 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 436 through 443 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: 3.511A pdb=" N ALA E 502 " --> pdb=" O LYS E 498 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG E 503 " --> pdb=" O GLN E 499 " (cutoff:3.500A) Proline residue: E 508 - end of helix Processing helix chain 'E' and resid 524 through 533 Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.992A pdb=" N GLU E 544 " --> pdb=" O ARG E 541 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG E 545 " --> pdb=" O GLY E 542 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP E 558 " --> pdb=" O ALA E 555 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E 559 " --> pdb=" O LYS E 556 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU E 560 " --> pdb=" O PHE E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 577 removed outlier: 4.316A pdb=" N ILE E 574 " --> pdb=" O ALA E 571 " (cutoff:3.500A) Proline residue: E 575 - end of helix No H-bonds generated for 'chain 'E' and resid 571 through 577' Processing helix chain 'E' and resid 585 through 588 Processing helix chain 'E' and resid 631 through 650 removed outlier: 4.158A pdb=" N THR E 642 " --> pdb=" O GLN E 638 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG E 645 " --> pdb=" O LEU E 641 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN E 649 " --> pdb=" O ARG E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 658 Processing helix chain 'E' and resid 681 through 692 Processing helix chain 'E' and resid 718 through 728 removed outlier: 3.578A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 removed outlier: 4.129A pdb=" N ALA E 741 " --> pdb=" O ASP E 738 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 743 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 762 through 769 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 removed outlier: 3.731A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU A 87 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.317A 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: 3.661A pdb=" N HIS A 377 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 6.964A 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: 6.601A 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: 3.576A 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: 5.791A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.416A 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: 3.855A pdb=" N GLN B 83 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 3.910A 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: 3.753A pdb=" N ILE B 44 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 69 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL B 70 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 5.435A 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 354 removed outlier: 7.926A pdb=" N LEU B 353 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR B 469 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS B 377 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 598 through 603 removed outlier: 3.655A pdb=" N ALA B 601 " --> pdb=" O THR B 608 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 608 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 623 through 626 removed outlier: 6.432A pdb=" N LEU B 663 " --> pdb=" O SER B 624 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR B 626 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL B 665 " --> pdb=" O THR B 626 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 700 through 702 removed outlier: 6.927A 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: 3.725A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 353 through 355 removed outlier: 6.252A pdb=" N ILE C 488 " --> pdb=" O VAL C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 376 through 380 removed outlier: 6.753A pdb=" N VAL C 418 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE C 379 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU C 420 " --> pdb=" O ILE C 379 " (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: 6.162A 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 705 through 707 removed outlier: 4.146A pdb=" N GLU C 705 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 103 through 106 removed outlier: 4.587A pdb=" N LEU D 103 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LEU D 43 " --> pdb=" O GLU D 4 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL D 47 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 23 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 73 through 77 removed outlier: 4.407A pdb=" N GLN D 73 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 85 " --> pdb=" O GLN D 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET D 75 " --> pdb=" O GLN D 83 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN D 83 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU D 77 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'D' and resid 350 through 352 Processing sheet with id= U, first strand: chain 'D' and resid 418 through 420 removed outlier: 7.240A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 520 through 522 removed outlier: 5.635A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 596 through 601 removed outlier: 3.561A pdb=" N ALA D 601 " --> pdb=" O THR D 608 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR D 608 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 622 through 624 Processing sheet with id= Y, first strand: chain 'D' and resid 734 through 736 removed outlier: 5.559A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 3 through 5 removed outlier: 3.869A pdb=" N LEU E 5 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 105 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP E 96 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 20 through 25 removed outlier: 3.655A pdb=" N GLU E 87 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN E 68 " --> pdb=" O ARG E 89 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ARG E 91 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY E 66 " --> pdb=" O ARG E 91 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 418 through 420 removed outlier: 7.553A pdb=" N PHE E 466 " --> pdb=" O ILE E 419 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.275A pdb=" N ARG E 567 " --> pdb=" O GLU E 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'E' and resid 732 through 736 removed outlier: 6.370A pdb=" N GLU E 755 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU E 735 " --> pdb=" O GLU E 755 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS E 757 " --> pdb=" O LEU E 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD 1062 hydrogen bonds defined for protein. 3027 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: 10.61 Time building geometry restraints manager: 12.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5772 1.32 - 1.45: 7324 1.45 - 1.58: 17713 1.58 - 1.70: 12 1.70 - 1.83: 210 Bond restraints: 31031 Sorted by residual: bond pdb=" C GLN E 229 " pdb=" O GLN E 229 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.78e+01 bond pdb=" CB MET D 427 " pdb=" CG MET D 427 " ideal model delta sigma weight residual 1.520 1.415 0.105 3.00e-02 1.11e+03 1.24e+01 bond pdb=" N ILE D 681 " pdb=" CA ILE D 681 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.26e-02 6.30e+03 9.09e+00 bond pdb=" N VAL A 54 " pdb=" CA VAL A 54 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.23e-02 6.61e+03 8.95e+00 bond pdb=" CA LEU C 421 " pdb=" CB LEU C 421 " ideal model delta sigma weight residual 1.526 1.481 0.046 1.53e-02 4.27e+03 8.91e+00 ... (remaining 31026 not shown) Histogram of bond angle deviations from ideal: 90.24 - 99.73: 24 99.73 - 109.22: 3537 109.22 - 118.71: 22186 118.71 - 128.20: 16076 128.20 - 137.69: 252 Bond angle restraints: 42075 Sorted by residual: angle pdb=" CA PRO A 714 " pdb=" N PRO A 714 " pdb=" CD PRO A 714 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.38e+01 angle pdb=" N GLY E 358 " pdb=" CA GLY E 358 " pdb=" C GLY E 358 " ideal model delta sigma weight residual 113.99 121.13 -7.14 1.28e+00 6.10e-01 3.11e+01 angle pdb=" N GLN E 229 " pdb=" CA GLN E 229 " pdb=" C GLN E 229 " ideal model delta sigma weight residual 110.97 104.97 6.00 1.09e+00 8.42e-01 3.03e+01 angle pdb=" C ALA A 400 " pdb=" N MET A 401 " pdb=" CA MET A 401 " ideal model delta sigma weight residual 122.90 111.57 11.33 2.07e+00 2.33e-01 2.99e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 107.70 101.40 6.30 1.22e+00 6.72e-01 2.66e+01 ... (remaining 42070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.63: 18706 30.63 - 61.25: 393 61.25 - 91.88: 42 91.88 - 122.50: 0 122.50 - 153.13: 3 Dihedral angle restraints: 19144 sinusoidal: 7989 harmonic: 11155 Sorted by residual: dihedral pdb=" C5' ADP D 801 " pdb=" O5' ADP D 801 " pdb=" PA ADP D 801 " pdb=" O2A ADP D 801 " ideal model delta sinusoidal sigma weight residual 300.00 146.88 153.13 1 2.00e+01 2.50e-03 4.54e+01 dihedral pdb=" O1B ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PB ADP C 801 " pdb=" PA ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 164.64 135.35 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" O2A ADP C 801 " pdb=" O3A ADP C 801 " pdb=" PA ADP C 801 " pdb=" PB ADP C 801 " ideal model delta sinusoidal sigma weight residual 300.00 172.24 127.76 1 2.00e+01 2.50e-03 3.87e+01 ... (remaining 19141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4352 0.110 - 0.221: 404 0.221 - 0.331: 28 0.331 - 0.442: 1 0.442 - 0.552: 1 Chirality restraints: 4786 Sorted by residual: chirality pdb=" CG LEU C 629 " pdb=" CB LEU C 629 " pdb=" CD1 LEU C 629 " pdb=" CD2 LEU C 629 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.63e+00 chirality pdb=" CG LEU A 751 " pdb=" CB LEU A 751 " pdb=" CD1 LEU A 751 " pdb=" CD2 LEU A 751 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CG LEU C 722 " pdb=" CB LEU C 722 " pdb=" CD1 LEU C 722 " pdb=" CD2 LEU C 722 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 4783 not shown) Planarity restraints: 5464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 713 " 0.069 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 714 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 714 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 714 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 171 " -0.023 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP E 171 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP E 171 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP E 171 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 171 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP E 171 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 171 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 171 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 171 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 228 " -0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLU E 228 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU E 228 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 229 " -0.019 2.00e-02 2.50e+03 ... (remaining 5461 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 2044 2.71 - 3.26: 32753 3.26 - 3.81: 54596 3.81 - 4.35: 67593 4.35 - 4.90: 104841 Nonbonded interactions: 261827 Sorted by model distance: nonbonded pdb=" O ALA D 639 " pdb=" OG1 THR D 642 " model vdw 2.167 2.440 nonbonded pdb=" O LEU D 528 " pdb=" OG SER D 532 " model vdw 2.177 2.440 nonbonded pdb=" O LEU D 364 " pdb=" OG SER D 367 " model vdw 2.185 2.440 nonbonded pdb=" O MET A 160 " pdb=" OG1 THR A 164 " model vdw 2.194 2.440 nonbonded pdb=" O ALA A 678 " pdb=" OG1 THR A 703 " model vdw 2.201 2.440 ... (remaining 261822 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 8.480 Check model and map are aligned: 0.480 Set scattering table: 0.290 Process input model: 81.980 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 31031 Z= 0.517 Angle : 1.265 17.891 42075 Z= 0.708 Chirality : 0.066 0.552 4786 Planarity : 0.008 0.098 5464 Dihedral : 13.225 153.127 11964 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.46 % Favored : 91.47 % Rotamer: Outliers : 0.12 % Allowed : 1.08 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.82 (0.12), residues: 3855 helix: -1.16 (0.12), residues: 1615 sheet: -2.43 (0.25), residues: 360 loop : -2.40 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP E 171 HIS 0.016 0.003 HIS B 407 PHE 0.050 0.003 PHE E 467 TYR 0.036 0.003 TYR C 460 ARG 0.030 0.001 ARG B 378 *********************** 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 217 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 3.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8354 (mmp) cc_final: 0.7993 (mmm) REVERT: A 698 MET cc_start: 0.4634 (mtt) cc_final: 0.3780 (mtt) REVERT: B 230 MET cc_start: 0.8760 (ttp) cc_final: 0.8456 (ppp) REVERT: B 351 LEU cc_start: 0.9292 (tp) cc_final: 0.9067 (tp) REVERT: B 379 ILE cc_start: 0.9565 (tp) cc_final: 0.9250 (tt) REVERT: B 409 MET cc_start: 0.9057 (tpt) cc_final: 0.8479 (tpp) REVERT: C 422 ASP cc_start: 0.8557 (t70) cc_final: 0.8338 (t0) REVERT: C 476 THR cc_start: 0.8976 (t) cc_final: 0.8743 (p) REVERT: C 483 ASP cc_start: 0.8804 (p0) cc_final: 0.8536 (p0) REVERT: C 711 LYS cc_start: 0.8909 (mptt) cc_final: 0.8680 (mmmt) REVERT: D 230 MET cc_start: 0.8295 (tmm) cc_final: 0.7813 (tmm) REVERT: D 317 GLU cc_start: 0.8345 (pp20) cc_final: 0.8084 (pp20) REVERT: D 401 MET cc_start: 0.9120 (ttp) cc_final: 0.8899 (pmm) REVERT: D 713 MET cc_start: 0.8723 (tpt) cc_final: 0.8471 (tpp) REVERT: E 255 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: E 657 PHE cc_start: 0.9066 (t80) cc_final: 0.8640 (t80) outliers start: 4 outliers final: 1 residues processed: 217 average time/residue: 0.4254 time to fit residues: 150.4717 Evaluate side-chains 175 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 255 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 50.0000 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 40.0000 chunk 301 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 349 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** C 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31031 Z= 0.208 Angle : 0.716 12.154 42075 Z= 0.357 Chirality : 0.045 0.192 4786 Planarity : 0.006 0.066 5464 Dihedral : 7.653 143.359 4304 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.68 % Allowed : 6.70 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.24 (0.13), residues: 3855 helix: -0.50 (0.12), residues: 1628 sheet: -2.23 (0.26), residues: 364 loop : -2.24 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 171 HIS 0.006 0.001 HIS B 407 PHE 0.017 0.001 PHE E 467 TYR 0.020 0.002 TYR D 643 ARG 0.010 0.000 ARG B 378 *********************** 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 200 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 MET cc_start: 0.8076 (mmp) cc_final: 0.7759 (mmm) REVERT: A 496 MET cc_start: 0.8464 (mmp) cc_final: 0.8211 (mmp) REVERT: B 351 LEU cc_start: 0.9327 (tp) cc_final: 0.9099 (tp) REVERT: C 258 MET cc_start: 0.4255 (mtt) cc_final: 0.3910 (mtt) REVERT: C 635 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8880 (pp20) REVERT: D 317 GLU cc_start: 0.8269 (pp20) cc_final: 0.8067 (pp20) REVERT: D 401 MET cc_start: 0.9044 (ttp) cc_final: 0.8817 (pmm) REVERT: D 516 MET cc_start: 0.7821 (ttm) cc_final: 0.6529 (mmm) REVERT: D 713 MET cc_start: 0.8493 (tpt) cc_final: 0.8251 (tpp) REVERT: D 727 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.5057 (mm-40) REVERT: E 276 MET cc_start: 0.4679 (OUTLIER) cc_final: 0.4415 (mmm) REVERT: E 427 MET cc_start: 0.8507 (tpt) cc_final: 0.8084 (mmm) REVERT: E 516 MET cc_start: 0.1249 (mtm) cc_final: 0.1039 (mtt) REVERT: E 657 PHE cc_start: 0.9065 (t80) cc_final: 0.8623 (t80) outliers start: 22 outliers final: 12 residues processed: 191 average time/residue: 0.3840 time to fit residues: 123.5238 Evaluate side-chains 181 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 276 MET Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 238 optimal weight: 30.0000 chunk 96 optimal weight: 50.0000 chunk 350 optimal weight: 10.0000 chunk 378 optimal weight: 1.9990 chunk 311 optimal weight: 40.0000 chunk 347 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN B 229 GLN B 454 HIS ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31031 Z= 0.358 Angle : 0.819 12.757 42075 Z= 0.413 Chirality : 0.046 0.194 4786 Planarity : 0.006 0.071 5464 Dihedral : 7.768 145.731 4302 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 33.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.98 % Allowed : 9.72 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.23 (0.13), residues: 3855 helix: -0.47 (0.12), residues: 1643 sheet: -2.17 (0.26), residues: 359 loop : -2.29 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 298 HIS 0.011 0.002 HIS B 407 PHE 0.018 0.002 PHE E 467 TYR 0.035 0.002 TYR D 643 ARG 0.013 0.001 ARG B 378 *********************** 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 234 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 170 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.4621 (pm20) REVERT: A 85 MET cc_start: 0.8110 (mmp) cc_final: 0.7869 (mmm) REVERT: B 439 MET cc_start: 0.9239 (tmm) cc_final: 0.8960 (tmm) REVERT: C 258 MET cc_start: 0.3440 (mtt) cc_final: 0.3106 (mtt) REVERT: C 422 ASP cc_start: 0.8266 (t0) cc_final: 0.8028 (t0) REVERT: C 439 MET cc_start: 0.9800 (mmm) cc_final: 0.9552 (mmm) REVERT: C 697 ARG cc_start: 0.0522 (OUTLIER) cc_final: -0.1546 (ptm160) REVERT: D 401 MET cc_start: 0.9028 (ttp) cc_final: 0.8815 (pmm) REVERT: D 499 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7844 (mm-40) REVERT: D 531 ILE cc_start: 0.9025 (mp) cc_final: 0.8632 (mp) REVERT: D 713 MET cc_start: 0.8676 (tpt) cc_final: 0.8347 (tpp) REVERT: E 75 MET cc_start: 0.6316 (ppp) cc_final: 0.5833 (ppp) REVERT: E 423 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: E 657 PHE cc_start: 0.9120 (t80) cc_final: 0.8771 (t80) outliers start: 64 outliers final: 31 residues processed: 220 average time/residue: 0.4012 time to fit residues: 147.0172 Evaluate side-chains 193 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 158 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 697 ARG Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 667 VAL Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 612 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 235 optimal weight: 50.0000 chunk 351 optimal weight: 9.9990 chunk 372 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 333 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN D 593 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31031 Z= 0.274 Angle : 0.736 12.217 42075 Z= 0.366 Chirality : 0.045 0.243 4786 Planarity : 0.005 0.055 5464 Dihedral : 7.593 139.907 4302 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 30.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.04 % Allowed : 12.47 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.04 (0.13), residues: 3855 helix: -0.27 (0.13), residues: 1637 sheet: -2.21 (0.25), residues: 379 loop : -2.18 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 298 HIS 0.010 0.002 HIS B 407 PHE 0.013 0.001 PHE D 467 TYR 0.023 0.002 TYR D 643 ARG 0.009 0.000 ARG B 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 233 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 167 time to evaluate : 3.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6345 (OUTLIER) cc_final: 0.4650 (pm20) REVERT: A 85 MET cc_start: 0.8108 (mmp) cc_final: 0.7874 (mmm) REVERT: A 160 MET cc_start: 0.7672 (mmm) cc_final: 0.7470 (mmm) REVERT: A 427 MET cc_start: 0.3789 (tpt) cc_final: 0.3362 (tpt) REVERT: A 496 MET cc_start: 0.8420 (mmp) cc_final: 0.8154 (mmp) REVERT: B 635 GLU cc_start: 0.9141 (pp20) cc_final: 0.8938 (pp20) REVERT: C 160 MET cc_start: 0.7740 (mmp) cc_final: 0.7398 (mmp) REVERT: C 258 MET cc_start: 0.3553 (mtt) cc_final: 0.3312 (mtt) REVERT: C 422 ASP cc_start: 0.8429 (t0) cc_final: 0.8189 (t0) REVERT: C 439 MET cc_start: 0.9802 (mmm) cc_final: 0.9571 (mmm) REVERT: C 512 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: C 756 ILE cc_start: 0.2707 (OUTLIER) cc_final: 0.2399 (mm) REVERT: D 401 MET cc_start: 0.8982 (ttp) cc_final: 0.8736 (pmm) REVERT: D 499 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7739 (mm-40) REVERT: D 531 ILE cc_start: 0.8938 (mp) cc_final: 0.8490 (mp) REVERT: D 713 MET cc_start: 0.8653 (tpt) cc_final: 0.8343 (tpp) REVERT: E 256 VAL cc_start: 0.5466 (OUTLIER) cc_final: 0.3563 (t) REVERT: E 409 MET cc_start: 0.8639 (tpp) cc_final: 0.8436 (tpp) REVERT: E 657 PHE cc_start: 0.9066 (t80) cc_final: 0.8611 (t80) outliers start: 66 outliers final: 37 residues processed: 221 average time/residue: 0.3853 time to fit residues: 142.9104 Evaluate side-chains 200 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 608 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 647 HIS 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: 0.0980 chunk 5 optimal weight: 5.9990 chunk 277 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 317 optimal weight: 50.0000 chunk 257 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 7.9990 chunk 334 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 504 GLN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 373 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31031 Z= 0.337 Angle : 0.800 15.115 42075 Z= 0.397 Chirality : 0.046 0.253 4786 Planarity : 0.006 0.059 5464 Dihedral : 7.596 141.243 4299 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 35.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.32 % Favored : 89.68 % Rotamer: Outliers : 2.41 % Allowed : 14.41 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.09 (0.13), residues: 3855 helix: -0.34 (0.13), residues: 1613 sheet: -2.19 (0.27), residues: 353 loop : -2.19 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 298 HIS 0.010 0.002 HIS B 407 PHE 0.015 0.002 PHE D 467 TYR 0.030 0.002 TYR D 643 ARG 0.012 0.001 ARG D 479 *********************** 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 245 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 167 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.4915 (pm20) REVERT: A 85 MET cc_start: 0.8132 (mmp) cc_final: 0.7801 (mmm) REVERT: A 160 MET cc_start: 0.7672 (mmm) cc_final: 0.7427 (mmm) REVERT: A 427 MET cc_start: 0.4018 (tpt) cc_final: 0.3501 (tpt) REVERT: A 496 MET cc_start: 0.8535 (mmp) cc_final: 0.8214 (mmp) REVERT: A 625 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9173 (tp) REVERT: A 698 MET cc_start: 0.3580 (mtt) cc_final: 0.3366 (mtt) REVERT: B 217 MET cc_start: 0.7789 (ppp) cc_final: 0.7580 (ppp) REVERT: B 439 MET cc_start: 0.9185 (tmm) cc_final: 0.8571 (ppp) REVERT: B 567 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6990 (mtt-85) REVERT: C 422 ASP cc_start: 0.8488 (t0) cc_final: 0.8250 (t0) REVERT: C 439 MET cc_start: 0.9812 (mmm) cc_final: 0.9588 (mmm) REVERT: C 483 ASP cc_start: 0.8507 (p0) cc_final: 0.8307 (p0) REVERT: C 512 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8358 (ttp-110) REVERT: C 756 ILE cc_start: 0.3459 (OUTLIER) cc_final: 0.3032 (mm) REVERT: D 401 MET cc_start: 0.9031 (ttp) cc_final: 0.8636 (pmm) REVERT: D 586 ASP cc_start: 0.7478 (m-30) cc_final: 0.7141 (p0) REVERT: D 713 MET cc_start: 0.8779 (tpt) cc_final: 0.8439 (tpp) REVERT: E 256 VAL cc_start: 0.4321 (OUTLIER) cc_final: 0.3940 (t) REVERT: E 276 MET cc_start: 0.4448 (mmp) cc_final: 0.4211 (mmm) REVERT: E 409 MET cc_start: 0.9023 (tpp) cc_final: 0.8663 (tpp) REVERT: E 657 PHE cc_start: 0.9084 (t80) cc_final: 0.8728 (t80) outliers start: 78 outliers final: 45 residues processed: 233 average time/residue: 0.3977 time to fit residues: 156.4681 Evaluate side-chains 209 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 512 ARG 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 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 5.9990 chunk 335 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 91 optimal weight: 50.0000 chunk 372 optimal weight: 20.0000 chunk 309 optimal weight: 40.0000 chunk 172 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 666 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 31031 Z= 0.472 Angle : 0.952 14.460 42075 Z= 0.480 Chirality : 0.051 0.258 4786 Planarity : 0.007 0.075 5464 Dihedral : 8.180 148.874 4299 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 47.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 3.67 % Allowed : 15.22 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -2.55 (0.13), residues: 3855 helix: -0.82 (0.12), residues: 1617 sheet: -2.31 (0.27), residues: 345 loop : -2.38 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP E 298 HIS 0.015 0.003 HIS E 454 PHE 0.022 0.002 PHE D 467 TYR 0.038 0.003 TYR D 643 ARG 0.012 0.001 ARG D 567 *********************** 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 281 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 162 time to evaluate : 3.333 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 49 GLN cc_start: 0.6756 (OUTLIER) cc_final: 0.5181 (pm20) REVERT: A 160 MET cc_start: 0.7646 (mmm) cc_final: 0.7392 (mmm) REVERT: A 427 MET cc_start: 0.4732 (tpt) cc_final: 0.4204 (tpt) REVERT: A 496 MET cc_start: 0.8604 (mmp) cc_final: 0.8239 (mmp) REVERT: A 761 ASP cc_start: 0.7157 (OUTLIER) cc_final: 0.6355 (t70) REVERT: A 770 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7073 (mp) REVERT: B 351 LEU cc_start: 0.9369 (tp) cc_final: 0.8969 (tp) REVERT: B 410 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8738 (ttpt) REVERT: B 439 MET cc_start: 0.8881 (tmm) cc_final: 0.8655 (tmm) REVERT: B 516 MET cc_start: 0.8013 (tpp) cc_final: 0.7444 (tpp) REVERT: B 567 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6971 (mtt-85) REVERT: B 613 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: B 633 MET cc_start: 0.9070 (mmm) cc_final: 0.8555 (mmt) REVERT: C 143 ARG cc_start: 0.9432 (ttp80) cc_final: 0.8950 (tpm170) REVERT: C 439 MET cc_start: 0.9815 (mmm) cc_final: 0.9582 (mmm) REVERT: C 512 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8218 (mtt180) REVERT: C 635 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8990 (pp20) REVERT: C 756 ILE cc_start: 0.4878 (OUTLIER) cc_final: 0.4603 (mt) REVERT: D 401 MET cc_start: 0.8914 (ttp) cc_final: 0.8573 (pmm) REVERT: D 416 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8955 (p0) REVERT: D 586 ASP cc_start: 0.7202 (m-30) cc_final: 0.6773 (p0) REVERT: D 698 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5404 (tmm) REVERT: D 713 MET cc_start: 0.8937 (tpt) cc_final: 0.8597 (tpp) REVERT: E 75 MET cc_start: 0.5879 (ppp) cc_final: 0.5594 (pmm) REVERT: E 85 MET cc_start: 0.6848 (mmt) cc_final: 0.6435 (mmp) REVERT: E 409 MET cc_start: 0.9225 (tpp) cc_final: 0.8842 (tpp) REVERT: E 657 PHE cc_start: 0.9129 (t80) cc_final: 0.8766 (t80) outliers start: 119 outliers final: 69 residues processed: 264 average time/residue: 0.3701 time to fit residues: 164.8109 Evaluate side-chains 235 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 155 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 613 GLU Chi-restraints excluded: chain B residue 614 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 767 GLU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 756 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 416 ASN Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 727 GLN Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 485 MET Chi-restraints excluded: chain E residue 576 THR Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 698 MET Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 313 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 371 optimal weight: 10.0000 chunk 232 optimal weight: 0.0270 chunk 226 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN ** B 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 510 GLN ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 475 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31031 Z= 0.205 Angle : 0.746 14.775 42075 Z= 0.363 Chirality : 0.045 0.257 4786 Planarity : 0.005 0.065 5464 Dihedral : 7.394 136.080 4299 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 27.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.91 % Allowed : 17.41 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.93 (0.13), residues: 3855 helix: -0.18 (0.13), residues: 1610 sheet: -2.13 (0.26), residues: 379 loop : -2.10 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 507 HIS 0.013 0.001 HIS B 407 PHE 0.017 0.001 PHE E 376 TYR 0.017 0.001 TYR A 225 ARG 0.008 0.001 ARG D 479 *********************** 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 236 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7526 (ptp) cc_final: 0.7300 (pmm) REVERT: A 49 GLN cc_start: 0.6452 (OUTLIER) cc_final: 0.4751 (pm20) REVERT: A 160 MET cc_start: 0.7592 (mmm) cc_final: 0.7338 (mmm) REVERT: A 427 MET cc_start: 0.4331 (tpt) cc_final: 0.3793 (tpt) REVERT: A 496 MET cc_start: 0.8426 (mmp) cc_final: 0.8096 (mmp) REVERT: B 230 MET cc_start: 0.8299 (ptt) cc_final: 0.7923 (ppp) REVERT: B 516 MET cc_start: 0.7931 (tpp) cc_final: 0.7611 (tpp) REVERT: B 567 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6839 (mtt-85) REVERT: B 633 MET cc_start: 0.9006 (mmm) cc_final: 0.8586 (mmt) REVERT: B 663 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8055 (mm) REVERT: C 439 MET cc_start: 0.9823 (mmm) cc_final: 0.9489 (mmm) REVERT: C 683 MET cc_start: 0.8648 (ptp) cc_final: 0.8364 (pmm) REVERT: D 496 MET cc_start: 0.8916 (ptp) cc_final: 0.8708 (pmm) REVERT: D 586 ASP cc_start: 0.7333 (m-30) cc_final: 0.6787 (p0) REVERT: D 633 MET cc_start: 0.8735 (ptt) cc_final: 0.8529 (mmt) REVERT: D 713 MET cc_start: 0.8608 (tpt) cc_final: 0.8320 (tpp) REVERT: E 75 MET cc_start: 0.6113 (ppp) cc_final: 0.5702 (pmm) REVERT: E 85 MET cc_start: 0.6765 (mmt) cc_final: 0.6428 (mmp) REVERT: E 276 MET cc_start: 0.4380 (mmp) cc_final: 0.4118 (mmm) REVERT: E 409 MET cc_start: 0.9020 (tpp) cc_final: 0.8727 (tpp) REVERT: E 469 THR cc_start: 0.5278 (OUTLIER) cc_final: 0.4922 (p) REVERT: E 657 PHE cc_start: 0.9035 (t80) cc_final: 0.8650 (t80) outliers start: 62 outliers final: 34 residues processed: 228 average time/residue: 0.3872 time to fit residues: 149.9769 Evaluate side-chains 199 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 161 time to evaluate : 3.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 733 ILE Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 40.0000 chunk 252 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 291 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31031 Z= 0.198 Angle : 0.721 15.367 42075 Z= 0.346 Chirality : 0.044 0.332 4786 Planarity : 0.005 0.069 5464 Dihedral : 7.109 134.856 4299 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 26.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.57 % Allowed : 17.93 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.67 (0.14), residues: 3855 helix: 0.05 (0.13), residues: 1605 sheet: -1.94 (0.26), residues: 374 loop : -1.98 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 507 HIS 0.012 0.001 HIS B 407 PHE 0.011 0.001 PHE E 376 TYR 0.014 0.001 TYR E 224 ARG 0.009 0.000 ARG D 479 *********************** 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 218 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 167 time to evaluate : 3.660 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 49 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.4892 (pm20) REVERT: A 85 MET cc_start: 0.8002 (mmp) cc_final: 0.7664 (mmm) REVERT: A 160 MET cc_start: 0.7545 (mmm) cc_final: 0.7288 (mmm) REVERT: A 427 MET cc_start: 0.4646 (tpt) cc_final: 0.4072 (tpt) REVERT: A 496 MET cc_start: 0.8424 (mmp) cc_final: 0.8090 (mmp) REVERT: B 230 MET cc_start: 0.8273 (ptt) cc_final: 0.7878 (ppp) REVERT: B 516 MET cc_start: 0.7794 (tpp) cc_final: 0.7503 (tpp) REVERT: B 567 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6876 (mtt-85) REVERT: B 625 LEU cc_start: 0.8829 (mp) cc_final: 0.8388 (tp) REVERT: B 633 MET cc_start: 0.9205 (mmm) cc_final: 0.8691 (mmt) REVERT: B 663 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8238 (mm) REVERT: C 143 ARG cc_start: 0.9402 (tmm160) cc_final: 0.8805 (tpm170) REVERT: C 439 MET cc_start: 0.9811 (mmm) cc_final: 0.9462 (mmm) REVERT: C 635 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8774 (pp20) REVERT: C 683 MET cc_start: 0.8729 (ptp) cc_final: 0.8024 (pmm) REVERT: D 499 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: D 586 ASP cc_start: 0.7172 (m-30) cc_final: 0.6542 (p0) REVERT: D 633 MET cc_start: 0.8660 (ptt) cc_final: 0.8367 (mmt) REVERT: D 713 MET cc_start: 0.8662 (tpt) cc_final: 0.8405 (tpp) REVERT: E 75 MET cc_start: 0.6077 (ppp) cc_final: 0.5700 (pmm) REVERT: E 85 MET cc_start: 0.6706 (mmt) cc_final: 0.6365 (mmp) REVERT: E 276 MET cc_start: 0.4394 (mmp) cc_final: 0.4131 (mmm) REVERT: E 409 MET cc_start: 0.8948 (tpp) cc_final: 0.8582 (tpp) REVERT: E 427 MET cc_start: 0.8548 (mmm) cc_final: 0.8197 (mmm) REVERT: E 469 THR cc_start: 0.5033 (OUTLIER) cc_final: 0.4673 (p) REVERT: E 657 PHE cc_start: 0.9003 (t80) cc_final: 0.8598 (t80) outliers start: 51 outliers final: 36 residues processed: 206 average time/residue: 0.4115 time to fit residues: 140.3874 Evaluate side-chains 203 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.8980 chunk 355 optimal weight: 6.9990 chunk 324 optimal weight: 50.0000 chunk 345 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 271 optimal weight: 0.2980 chunk 106 optimal weight: 3.9990 chunk 312 optimal weight: 40.0000 chunk 327 optimal weight: 30.0000 chunk 344 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 727 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 742 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31031 Z= 0.189 Angle : 0.722 15.633 42075 Z= 0.345 Chirality : 0.044 0.285 4786 Planarity : 0.005 0.069 5464 Dihedral : 6.950 134.071 4299 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 25.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.64 % Allowed : 18.21 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.55 (0.14), residues: 3855 helix: 0.17 (0.13), residues: 1613 sheet: -1.98 (0.26), residues: 396 loop : -1.91 (0.15), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 507 HIS 0.013 0.001 HIS B 407 PHE 0.007 0.001 PHE D 657 TYR 0.016 0.001 TYR C 332 ARG 0.007 0.000 ARG D 479 *********************** 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 221 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 3.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6225 (OUTLIER) cc_final: 0.4742 (pm20) REVERT: A 85 MET cc_start: 0.7946 (mmp) cc_final: 0.7577 (mmm) REVERT: A 160 MET cc_start: 0.7533 (mmm) cc_final: 0.7266 (mmm) REVERT: A 427 MET cc_start: 0.4817 (tpt) cc_final: 0.4155 (tpt) REVERT: A 496 MET cc_start: 0.8424 (mmp) cc_final: 0.8097 (mmp) REVERT: B 516 MET cc_start: 0.7705 (tpp) cc_final: 0.7463 (tpp) REVERT: B 567 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6896 (mtt-85) REVERT: B 625 LEU cc_start: 0.8729 (mp) cc_final: 0.8393 (tp) REVERT: B 663 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8229 (mm) REVERT: C 143 ARG cc_start: 0.9400 (tmm160) cc_final: 0.8815 (tpm170) REVERT: C 439 MET cc_start: 0.9811 (mmm) cc_final: 0.9363 (mmm) REVERT: C 635 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8729 (pp20) REVERT: D 499 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8112 (mm-40) REVERT: D 633 MET cc_start: 0.8623 (ptt) cc_final: 0.8297 (mmp) REVERT: D 713 MET cc_start: 0.8681 (tpt) cc_final: 0.8408 (tpp) REVERT: E 75 MET cc_start: 0.5983 (ppp) cc_final: 0.5703 (pmm) REVERT: E 85 MET cc_start: 0.6679 (mmt) cc_final: 0.6319 (mmp) REVERT: E 276 MET cc_start: 0.4263 (mmp) cc_final: 0.3992 (mmm) REVERT: E 401 MET cc_start: 0.7950 (tpp) cc_final: 0.7513 (mmm) REVERT: E 409 MET cc_start: 0.8969 (tpp) cc_final: 0.8607 (tpp) REVERT: E 427 MET cc_start: 0.8615 (mmm) cc_final: 0.8294 (mmm) REVERT: E 469 THR cc_start: 0.4654 (OUTLIER) cc_final: 0.4277 (p) REVERT: E 657 PHE cc_start: 0.9065 (t80) cc_final: 0.8678 (t80) outliers start: 53 outliers final: 42 residues processed: 208 average time/residue: 0.3891 time to fit residues: 135.9332 Evaluate side-chains 212 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 164 time to evaluate : 3.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 472 ASN Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 320 TYR Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9990 chunk 365 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 40.0000 chunk 254 optimal weight: 2.9990 chunk 383 optimal weight: 7.9990 chunk 353 optimal weight: 8.9990 chunk 305 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 235 optimal weight: 6.9990 chunk 187 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31031 Z= 0.310 Angle : 0.800 12.162 42075 Z= 0.392 Chirality : 0.046 0.310 4786 Planarity : 0.006 0.059 5464 Dihedral : 7.224 131.151 4299 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 34.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 1.76 % Allowed : 18.21 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % 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: -1.76 (0.14), residues: 3855 helix: -0.08 (0.13), residues: 1626 sheet: -1.96 (0.26), residues: 380 loop : -1.99 (0.15), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 298 HIS 0.012 0.002 HIS B 407 PHE 0.013 0.002 PHE A 466 TYR 0.027 0.002 TYR D 643 ARG 0.013 0.001 ARG B 479 ********************** 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 221 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 164 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.4945 (pm20) REVERT: A 85 MET cc_start: 0.8040 (mmp) cc_final: 0.7682 (mmm) REVERT: A 160 MET cc_start: 0.7544 (mmm) cc_final: 0.7272 (mmm) REVERT: A 427 MET cc_start: 0.4691 (tpt) cc_final: 0.3993 (tpt) REVERT: A 496 MET cc_start: 0.8509 (mmp) cc_final: 0.8152 (mmp) REVERT: B 516 MET cc_start: 0.8008 (tpp) cc_final: 0.7781 (tpp) REVERT: B 567 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7030 (mtt-85) REVERT: B 625 LEU cc_start: 0.8791 (mp) cc_final: 0.8557 (tp) REVERT: B 663 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8124 (mm) REVERT: C 143 ARG cc_start: 0.9373 (tmm160) cc_final: 0.8797 (tpm170) REVERT: C 421 LEU cc_start: 0.9399 (mt) cc_final: 0.9156 (mp) REVERT: C 439 MET cc_start: 0.9810 (mmm) cc_final: 0.9447 (mmm) REVERT: C 698 MET cc_start: -0.0264 (mmt) cc_final: -0.0823 (mmt) REVERT: D 499 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8214 (mm-40) REVERT: D 713 MET cc_start: 0.8833 (tpt) cc_final: 0.8579 (tpp) REVERT: E 85 MET cc_start: 0.6725 (mmt) cc_final: 0.6437 (mmp) REVERT: E 276 MET cc_start: 0.4272 (mmp) cc_final: 0.3991 (mmm) REVERT: E 409 MET cc_start: 0.9128 (tpp) cc_final: 0.8690 (tpp) REVERT: E 657 PHE cc_start: 0.9062 (t80) cc_final: 0.8684 (t80) outliers start: 57 outliers final: 45 residues processed: 208 average time/residue: 0.3917 time to fit residues: 136.3419 Evaluate side-chains 210 residues out of total 3240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 228 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 453 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain C residue 490 ILE Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 635 GLU Chi-restraints excluded: chain C residue 742 GLN Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 499 GLN Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 372 MET Chi-restraints excluded: chain E residue 469 THR Chi-restraints excluded: chain E residue 476 THR Chi-restraints excluded: chain E residue 583 TYR Chi-restraints excluded: chain E residue 612 ILE Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 647 HIS Chi-restraints excluded: chain E residue 723 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 50.0000 chunk 325 optimal weight: 8.9990 chunk 93 optimal weight: 50.0000 chunk 281 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 0.0040 chunk 128 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 638 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.097416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.070169 restraints weight = 283071.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.068644 restraints weight = 235861.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.068478 restraints weight = 178173.238| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31031 Z= 0.212 Angle : 0.743 16.977 42075 Z= 0.356 Chirality : 0.045 0.307 4786 Planarity : 0.005 0.057 5464 Dihedral : 7.038 133.107 4299 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 27.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 1.60 % Allowed : 18.49 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3855 helix: 0.12 (0.13), residues: 1613 sheet: -2.03 (0.26), residues: 379 loop : -1.88 (0.15), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 298 HIS 0.012 0.001 HIS B 407 PHE 0.008 0.001 PHE D 376 TYR 0.014 0.001 TYR E 224 ARG 0.006 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5565.02 seconds wall clock time: 102 minutes 25.18 seconds (6145.18 seconds total)