Starting phenix.real_space_refine on Fri Feb 16 22:21:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuv_34112/02_2024/7yuv_34112_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuv_34112/02_2024/7yuv_34112.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/7yuv_34112/02_2024/7yuv_34112.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuv_34112/02_2024/7yuv_34112.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuv_34112/02_2024/7yuv_34112_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yuv_34112/02_2024/7yuv_34112_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= 0.002 sd= 0.040 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 6 5.49 5 S 60 5.16 5 C 10510 2.51 5 N 2919 2.21 5 O 3162 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 745": "OE1" <-> "OE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "D TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16657 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "B" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "D" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} 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} Time building chain proxies: 8.91, per 1000 atoms: 0.53 Number of scatterers: 16657 At special positions: 0 Unit cell: (113.98, 106.6, 141.86, 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 60 16.00 P 6 15.00 O 3162 8.00 N 2919 7.00 C 10510 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: 6.89 Conformation dependent library (CDL) restraints added in 3.1 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 19 sheets defined 39.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.62 Creating SS restraints... Processing helix chain 'A' and resid 246 through 255 removed outlier: 4.850A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.800A pdb=" N THR A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 Processing helix chain 'A' and resid 325 through 333 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 411 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 495 through 505 Processing helix chain 'A' and resid 507 through 513 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 541 through 560 Processing helix chain 'A' and resid 571 through 578 removed outlier: 3.587A pdb=" N ILE A 574 " --> pdb=" O ALA A 571 " (cutoff:3.500A) Proline residue: A 575 - end of helix removed outlier: 3.512A pdb=" N LEU A 578 " --> pdb=" O PRO A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 571 through 578' Processing helix chain 'A' and resid 631 through 646 removed outlier: 3.574A pdb=" N ALA A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 718 through 728 Processing helix chain 'A' and resid 737 through 744 removed outlier: 4.032A pdb=" N GLU A 740 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALA A 741 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 767 Processing helix chain 'B' and resid 244 through 255 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 323 through 338 removed outlier: 4.086A pdb=" N ARG B 328 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE B 329 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 436 through 443 Processing helix chain 'B' and resid 479 through 482 Processing helix chain 'B' and resid 495 through 504 removed outlier: 3.526A pdb=" N GLN B 504 " --> pdb=" O ALA B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 513 Processing helix chain 'B' and resid 524 through 533 Processing helix chain 'B' and resid 541 through 559 removed outlier: 3.515A pdb=" N ARG B 545 " --> pdb=" O ARG B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 578 No H-bonds generated for 'chain 'B' and resid 575 through 578' Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 631 through 647 Processing helix chain 'B' and resid 680 through 692 Processing helix chain 'B' and resid 720 through 727 Processing helix chain 'B' and resid 737 through 745 removed outlier: 4.560A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU B 744 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 762 through 768 removed outlier: 4.200A pdb=" N GLU B 767 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 768 " --> pdb=" O GLU B 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 260 through 273 removed outlier: 3.790A pdb=" N LYS C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.529A pdb=" N VAL C 285 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR C 294 " --> pdb=" O ASP C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 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 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 424 through 426 No H-bonds generated for 'chain 'C' and resid 424 through 426' Processing helix chain 'C' and resid 435 through 443 removed outlier: 4.399A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.709A pdb=" N ASN C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR C 450 " --> pdb=" O GLU C 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 445 through 450' Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 506 through 514 Processing helix chain 'C' and resid 524 through 534 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 587 through 590 Processing helix chain 'C' and resid 631 through 646 Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 680 through 692 Processing helix chain 'C' and resid 718 through 728 Processing helix chain 'C' and resid 737 through 743 removed outlier: 4.502A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 769 removed outlier: 3.748A pdb=" N LEU C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 Processing helix chain 'D' and resid 260 through 274 removed outlier: 3.546A pdb=" N GLU D 274 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.467A pdb=" N GLU D 317 " --> pdb=" O GLN D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 337 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.521A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 Processing helix chain 'D' and resid 435 through 443 Processing helix chain 'D' and resid 479 through 482 No H-bonds generated for 'chain 'D' and resid 479 through 482' Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 506 through 513 Processing helix chain 'D' and resid 524 through 533 Processing helix chain 'D' and resid 541 through 559 Processing helix chain 'D' and resid 574 through 577 No H-bonds generated for 'chain 'D' and resid 574 through 577' Processing helix chain 'D' and resid 631 through 646 Processing helix chain 'D' and resid 680 through 692 Processing helix chain 'D' and resid 718 through 727 Processing helix chain 'D' and resid 737 through 745 removed outlier: 4.219A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 745 " --> pdb=" O GLN D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 753 Processing helix chain 'D' and resid 762 through 767 Processing sheet with id= A, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.431A pdb=" N ILE A 488 " --> pdb=" O VAL A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.731A pdb=" N PHE A 466 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU A 421 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ILE A 468 " --> pdb=" O LEU A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.087A pdb=" N ARG A 567 " --> pdb=" O GLU A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.730A pdb=" N THR A 608 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 613 through 618 removed outlier: 3.795A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 615 " --> pdb=" O HIS A 664 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 664 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 732 through 736 removed outlier: 5.973A pdb=" N GLU A 755 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU A 735 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 5.487A 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 376 through 380 removed outlier: 6.229A pdb=" N VAL B 418 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 379 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 420 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE B 468 " --> pdb=" O LEU B 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 597 through 603 removed outlier: 3.850A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 613 through 615 Processing sheet with id= J, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.607A pdb=" N GLU B 755 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 735 " --> pdb=" O GLU B 755 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 757 " --> pdb=" O LEU B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 485 through 487 removed outlier: 6.187A pdb=" N ILE C 350 " --> pdb=" O GLU C 486 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU C 351 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA C 471 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR C 470 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.659A pdb=" N ARG C 567 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.528A pdb=" N ALA C 601 " --> pdb=" O THR C 608 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 608 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 603 " --> pdb=" O GLY C 606 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 613 through 618 removed outlier: 3.694A pdb=" N HIS C 664 " --> pdb=" O ALA C 615 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL C 617 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS C 622 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL C 665 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.327A pdb=" N LYS C 732 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLU C 755 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEU C 735 " --> pdb=" O GLU C 755 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS C 757 " --> pdb=" O LEU C 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 376 through 378 removed outlier: 5.633A pdb=" N VAL D 418 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE D 466 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU D 421 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE D 468 " --> pdb=" O LEU D 421 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 520 through 522 removed outlier: 5.567A pdb=" N ARG D 567 " --> pdb=" O GLU D 521 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 596 through 603 removed outlier: 3.528A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 603 " --> pdb=" O GLY D 606 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.512A pdb=" N LYS D 732 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N GLU D 755 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU D 735 " --> pdb=" O GLU D 755 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LYS D 757 " --> pdb=" O LEU D 735 " (cutoff:3.500A) No H-bonds generated for sheet with id= S 504 hydrogen bonds defined for protein. 1386 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: 4.62 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5591 1.34 - 1.46: 2678 1.46 - 1.58: 8573 1.58 - 1.69: 9 1.69 - 1.81: 120 Bond restraints: 16971 Sorted by residual: bond pdb=" N LYS B 323 " pdb=" CA LYS B 323 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.76e+00 bond pdb=" C THR B 672 " pdb=" N PRO B 673 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" C4 ADP B 801 " pdb=" C5 ADP B 801 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.37e+00 bond pdb=" C4 ADP C 801 " pdb=" C5 ADP C 801 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" C THR A 672 " pdb=" O THR A 672 " ideal model delta sigma weight residual 1.234 1.240 -0.005 5.00e-03 4.00e+04 1.08e+00 ... (remaining 16966 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.94: 553 105.94 - 113.56: 9649 113.56 - 121.17: 8146 121.17 - 128.79: 4544 128.79 - 136.40: 127 Bond angle restraints: 23019 Sorted by residual: angle pdb=" N VAL A 605 " pdb=" CA VAL A 605 " pdb=" C VAL A 605 " ideal model delta sigma weight residual 111.91 106.84 5.07 8.90e-01 1.26e+00 3.24e+01 angle pdb=" C LEU A 322 " pdb=" CA LEU A 322 " pdb=" CB LEU A 322 " ideal model delta sigma weight residual 117.23 109.86 7.37 1.36e+00 5.41e-01 2.94e+01 angle pdb=" CA LEU A 322 " pdb=" C LEU A 322 " pdb=" N LYS A 323 " ideal model delta sigma weight residual 119.98 116.23 3.75 8.50e-01 1.38e+00 1.95e+01 angle pdb=" C LYS C 556 " pdb=" CA LYS C 556 " pdb=" CB LYS C 556 " ideal model delta sigma weight residual 110.92 105.12 5.80 1.59e+00 3.96e-01 1.33e+01 angle pdb=" N GLY C 539 " pdb=" CA GLY C 539 " pdb=" C GLY C 539 " ideal model delta sigma weight residual 111.21 114.99 -3.78 1.04e+00 9.25e-01 1.32e+01 ... (remaining 23014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.90: 10081 28.90 - 57.80: 303 57.80 - 86.70: 28 86.70 - 115.59: 4 115.59 - 144.49: 5 Dihedral angle restraints: 10421 sinusoidal: 4333 harmonic: 6088 Sorted by residual: dihedral pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C4 ADP B 801 " ideal model delta sinusoidal sigma weight residual 91.55 -123.96 -144.49 1 2.00e+01 2.50e-03 4.35e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 171.53 128.47 1 2.00e+01 2.50e-03 3.89e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 65.30 -125.30 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 10418 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1860 0.043 - 0.086: 553 0.086 - 0.130: 186 0.130 - 0.173: 16 0.173 - 0.216: 1 Chirality restraints: 2616 Sorted by residual: chirality pdb=" CB ILE A 424 " pdb=" CA ILE A 424 " pdb=" CG1 ILE A 424 " pdb=" CG2 ILE A 424 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU C 743 " pdb=" CB LEU C 743 " pdb=" CD1 LEU C 743 " pdb=" CD2 LEU C 743 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.89e-01 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2613 not shown) Planarity restraints: 2975 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 617 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 618 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 618 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 618 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 557 " 0.009 2.00e-02 2.50e+03 1.29e-02 2.89e+00 pdb=" CG PHE D 557 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE D 557 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE D 557 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 557 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 557 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 557 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 558 " 0.013 2.00e-02 2.50e+03 9.69e-03 2.35e+00 pdb=" CG TRP B 558 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP B 558 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 558 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 558 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 558 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 558 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 558 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 558 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 558 " 0.000 2.00e-02 2.50e+03 ... (remaining 2972 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 429 2.69 - 3.24: 17227 3.24 - 3.80: 26965 3.80 - 4.35: 35594 4.35 - 4.90: 56177 Nonbonded interactions: 136392 Sorted by model distance: nonbonded pdb=" NE2 GLN A 510 " pdb=" O GLU A 544 " model vdw 2.141 2.520 nonbonded pdb=" OE1 GLN C 277 " pdb=" OG1 THR C 284 " model vdw 2.154 2.440 nonbonded pdb=" OG1 THR B 603 " pdb=" O GLY B 606 " model vdw 2.154 2.440 nonbonded pdb=" O LYS C 587 " pdb=" OG1 THR C 590 " model vdw 2.170 2.440 nonbonded pdb=" O ARG C 512 " pdb=" NE2 GLN D 340 " model vdw 2.177 2.520 ... (remaining 136387 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 243 through 774) selection = (chain 'B' and resid 243 through 774) selection = (chain 'C' and resid 243 through 774) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.620 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 44.990 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16971 Z= 0.182 Angle : 0.672 8.362 23019 Z= 0.337 Chirality : 0.045 0.216 2616 Planarity : 0.004 0.054 2975 Dihedral : 13.834 144.492 6517 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.33 (0.19), residues: 2120 helix: 0.43 (0.19), residues: 838 sheet: -2.04 (0.32), residues: 260 loop : -1.67 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 558 HIS 0.007 0.001 HIS C 377 PHE 0.029 0.002 PHE D 557 TYR 0.018 0.001 TYR C 643 ARG 0.008 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 2.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 LEU cc_start: 0.6089 (mt) cc_final: 0.5870 (mt) REVERT: C 568 THR cc_start: 0.8142 (m) cc_final: 0.7559 (p) outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.2747 time to fit residues: 104.7722 Evaluate side-chains 183 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 20.0000 chunk 160 optimal weight: 40.0000 chunk 89 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 0.0000 chunk 192 optimal weight: 8.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 GLN C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16971 Z= 0.322 Angle : 0.706 8.727 23019 Z= 0.342 Chirality : 0.046 0.162 2616 Planarity : 0.005 0.061 2975 Dihedral : 8.256 145.548 2357 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 1.30 % Allowed : 10.05 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.64 (0.18), residues: 2120 helix: 0.05 (0.18), residues: 851 sheet: -2.15 (0.31), residues: 264 loop : -1.77 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 558 HIS 0.008 0.002 HIS C 726 PHE 0.024 0.003 PHE D 557 TYR 0.019 0.002 TYR B 658 ARG 0.006 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 200 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 558 TRP cc_start: 0.7494 (t60) cc_final: 0.7214 (t60) REVERT: D 633 MET cc_start: 0.2438 (mmt) cc_final: 0.2221 (mmt) REVERT: D 666 HIS cc_start: 0.5155 (OUTLIER) cc_final: 0.4560 (m-70) outliers start: 23 outliers final: 17 residues processed: 211 average time/residue: 0.2871 time to fit residues: 92.1028 Evaluate side-chains 195 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 659 ASN Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 0.2980 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 30.0000 chunk 208 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16971 Z= 0.214 Angle : 0.641 10.507 23019 Z= 0.306 Chirality : 0.044 0.165 2616 Planarity : 0.004 0.057 2975 Dihedral : 8.020 146.879 2357 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.41 % Allowed : 14.16 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.46 (0.19), residues: 2120 helix: 0.23 (0.18), residues: 844 sheet: -2.11 (0.32), residues: 259 loop : -1.67 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 558 HIS 0.006 0.001 HIS B 319 PHE 0.018 0.002 PHE D 557 TYR 0.021 0.002 TYR C 768 ARG 0.005 0.000 ARG C 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 558 TRP cc_start: 0.7454 (t60) cc_final: 0.7234 (t60) REVERT: D 258 MET cc_start: 0.2465 (mmt) cc_final: 0.1840 (mmm) REVERT: D 633 MET cc_start: 0.2396 (mmt) cc_final: 0.2155 (mmt) REVERT: D 666 HIS cc_start: 0.5020 (OUTLIER) cc_final: 0.4498 (m-70) outliers start: 25 outliers final: 19 residues processed: 213 average time/residue: 0.2928 time to fit residues: 94.3600 Evaluate side-chains 200 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 193 optimal weight: 20.0000 chunk 204 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16971 Z= 0.184 Angle : 0.621 10.582 23019 Z= 0.295 Chirality : 0.043 0.152 2616 Planarity : 0.004 0.055 2975 Dihedral : 7.788 147.357 2357 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.58 % Allowed : 14.67 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.32 (0.19), residues: 2120 helix: 0.38 (0.19), residues: 844 sheet: -2.01 (0.32), residues: 249 loop : -1.66 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 558 HIS 0.014 0.001 HIS B 726 PHE 0.015 0.002 PHE D 557 TYR 0.025 0.001 TYR B 768 ARG 0.006 0.000 ARG C 529 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 423 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: C 262 VAL cc_start: 0.5548 (OUTLIER) cc_final: 0.5326 (t) REVERT: D 258 MET cc_start: 0.2715 (mmt) cc_final: 0.2161 (mmm) REVERT: D 666 HIS cc_start: 0.5019 (OUTLIER) cc_final: 0.4576 (m-70) outliers start: 28 outliers final: 18 residues processed: 217 average time/residue: 0.2970 time to fit residues: 97.9548 Evaluate side-chains 207 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 152 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16971 Z= 0.333 Angle : 0.714 9.702 23019 Z= 0.345 Chirality : 0.046 0.212 2616 Planarity : 0.005 0.062 2975 Dihedral : 7.889 148.282 2357 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.88 % Allowed : 15.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.64 (0.19), residues: 2120 helix: 0.10 (0.18), residues: 849 sheet: -2.22 (0.30), residues: 268 loop : -1.79 (0.20), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 563 HIS 0.015 0.002 HIS B 726 PHE 0.018 0.003 PHE C 466 TYR 0.023 0.002 TYR B 768 ARG 0.006 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 197 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 702 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7461 (ptp) REVERT: B 708 LEU cc_start: 0.7777 (tt) cc_final: 0.7475 (mp) REVERT: C 262 VAL cc_start: 0.5562 (OUTLIER) cc_final: 0.5346 (t) REVERT: C 331 GLU cc_start: 0.7210 (pt0) cc_final: 0.6808 (pt0) REVERT: C 499 GLN cc_start: 0.7689 (mt0) cc_final: 0.7381 (mt0) REVERT: D 666 HIS cc_start: 0.4892 (OUTLIER) cc_final: 0.4367 (m-70) outliers start: 51 outliers final: 32 residues processed: 234 average time/residue: 0.2844 time to fit residues: 100.2896 Evaluate side-chains 214 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 10.0000 chunk 184 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 205 optimal weight: 0.0470 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 107 optimal weight: 20.0000 overall best weight: 0.8482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS C 377 HIS ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16971 Z= 0.185 Angle : 0.644 13.257 23019 Z= 0.305 Chirality : 0.044 0.161 2616 Planarity : 0.004 0.057 2975 Dihedral : 7.578 150.722 2357 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.37 % Allowed : 16.76 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.42 (0.19), residues: 2120 helix: 0.31 (0.19), residues: 853 sheet: -2.20 (0.30), residues: 271 loop : -1.66 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 563 HIS 0.022 0.001 HIS B 726 PHE 0.012 0.001 PHE A 657 TYR 0.013 0.001 TYR C 768 ARG 0.005 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 200 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6531 (mtt) cc_final: 0.5482 (mtt) REVERT: B 493 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5538 (m-10) REVERT: B 702 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: B 708 LEU cc_start: 0.7638 (tt) cc_final: 0.7336 (mp) REVERT: C 262 VAL cc_start: 0.5745 (OUTLIER) cc_final: 0.5483 (t) REVERT: C 528 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (mp) REVERT: D 666 HIS cc_start: 0.5033 (OUTLIER) cc_final: 0.4584 (m-70) outliers start: 42 outliers final: 26 residues processed: 230 average time/residue: 0.2870 time to fit residues: 99.8963 Evaluate side-chains 212 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 181 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 528 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 172 optimal weight: 20.0000 chunk 114 optimal weight: 0.3980 chunk 204 optimal weight: 20.0000 chunk 127 optimal weight: 4.9990 chunk 124 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 HIS B 472 ASN B 726 HIS ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16971 Z= 0.184 Angle : 0.639 10.226 23019 Z= 0.302 Chirality : 0.044 0.154 2616 Planarity : 0.004 0.057 2975 Dihedral : 7.383 149.477 2357 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.26 % Allowed : 17.66 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.35 (0.19), residues: 2120 helix: 0.37 (0.19), residues: 856 sheet: -2.05 (0.31), residues: 253 loop : -1.70 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 563 HIS 0.021 0.001 HIS B 726 PHE 0.029 0.002 PHE A 657 TYR 0.016 0.001 TYR A 320 ARG 0.003 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6458 (mtt) cc_final: 0.5529 (mtt) REVERT: A 485 MET cc_start: 0.4161 (mmm) cc_final: 0.2142 (mtt) REVERT: A 611 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8340 (m) REVERT: B 493 TYR cc_start: 0.6305 (OUTLIER) cc_final: 0.5455 (m-10) REVERT: B 702 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7269 (ptp) REVERT: B 708 LEU cc_start: 0.7660 (tt) cc_final: 0.7329 (mp) REVERT: C 262 VAL cc_start: 0.5642 (OUTLIER) cc_final: 0.5441 (t) REVERT: C 702 MET cc_start: 0.7795 (ptp) cc_final: 0.7595 (ptp) REVERT: D 258 MET cc_start: 0.2459 (mmt) cc_final: 0.1829 (mmm) REVERT: D 666 HIS cc_start: 0.5137 (OUTLIER) cc_final: 0.4744 (m-70) outliers start: 40 outliers final: 29 residues processed: 228 average time/residue: 0.3138 time to fit residues: 106.7295 Evaluate side-chains 215 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 160 optimal weight: 0.0060 chunk 185 optimal weight: 1.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 HIS ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16971 Z= 0.198 Angle : 0.638 9.992 23019 Z= 0.303 Chirality : 0.044 0.152 2616 Planarity : 0.004 0.057 2975 Dihedral : 7.223 148.329 2357 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.48 % Allowed : 17.89 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.32 (0.19), residues: 2120 helix: 0.41 (0.19), residues: 850 sheet: -2.05 (0.31), residues: 253 loop : -1.67 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 602 HIS 0.018 0.001 HIS B 726 PHE 0.028 0.002 PHE A 657 TYR 0.011 0.001 TYR B 493 ARG 0.006 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 185 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 485 MET cc_start: 0.4024 (mmm) cc_final: 0.2119 (mtt) REVERT: A 611 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8356 (m) REVERT: A 698 MET cc_start: 0.7110 (tpp) cc_final: 0.6765 (tpp) REVERT: B 423 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6872 (tp30) REVERT: B 486 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: B 493 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5656 (m-10) REVERT: B 702 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7307 (ptp) REVERT: B 708 LEU cc_start: 0.7643 (tt) cc_final: 0.7361 (mp) REVERT: C 262 VAL cc_start: 0.5689 (OUTLIER) cc_final: 0.5464 (t) REVERT: D 258 MET cc_start: 0.2713 (mmt) cc_final: 0.2087 (mmm) REVERT: D 666 HIS cc_start: 0.5122 (OUTLIER) cc_final: 0.4738 (m-70) outliers start: 44 outliers final: 34 residues processed: 220 average time/residue: 0.3084 time to fit residues: 100.8447 Evaluate side-chains 222 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 486 GLU Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9990 chunk 178 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 chunk 189 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** C 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 HIS ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16971 Z= 0.204 Angle : 0.643 9.326 23019 Z= 0.305 Chirality : 0.044 0.208 2616 Planarity : 0.004 0.057 2975 Dihedral : 7.098 147.310 2357 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.54 % Allowed : 18.06 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.29 (0.19), residues: 2120 helix: 0.43 (0.19), residues: 849 sheet: -1.98 (0.32), residues: 250 loop : -1.67 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 563 HIS 0.008 0.001 HIS C 726 PHE 0.026 0.002 PHE A 657 TYR 0.018 0.001 TYR A 320 ARG 0.005 0.000 ARG A 645 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6425 (mtt) cc_final: 0.5370 (mtt) REVERT: A 351 LEU cc_start: 0.6926 (tp) cc_final: 0.6666 (tp) REVERT: A 485 MET cc_start: 0.4277 (mmm) cc_final: 0.2518 (mtt) REVERT: A 611 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (m) REVERT: A 698 MET cc_start: 0.7013 (tpp) cc_final: 0.6686 (tpp) REVERT: B 485 MET cc_start: 0.6539 (tpp) cc_final: 0.6039 (tpp) REVERT: B 493 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.5721 (m-10) REVERT: B 702 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7327 (ptp) REVERT: B 708 LEU cc_start: 0.7712 (tt) cc_final: 0.7463 (mp) REVERT: C 262 VAL cc_start: 0.5720 (OUTLIER) cc_final: 0.5495 (t) REVERT: D 258 MET cc_start: 0.2741 (mmt) cc_final: 0.2182 (mmm) REVERT: D 666 HIS cc_start: 0.5102 (OUTLIER) cc_final: 0.4756 (m-70) outliers start: 45 outliers final: 34 residues processed: 221 average time/residue: 0.3081 time to fit residues: 101.6891 Evaluate side-chains 218 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 179 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 675 ASP Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 449 ASN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 765 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 0.0040 chunk 211 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 ASN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16971 Z= 0.173 Angle : 0.633 9.402 23019 Z= 0.299 Chirality : 0.044 0.193 2616 Planarity : 0.004 0.057 2975 Dihedral : 6.988 149.681 2357 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.14 % Allowed : 18.62 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.22 (0.19), residues: 2120 helix: 0.49 (0.19), residues: 850 sheet: -1.97 (0.31), residues: 256 loop : -1.61 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 563 HIS 0.007 0.001 HIS C 726 PHE 0.025 0.001 PHE A 657 TYR 0.015 0.001 TYR A 658 ARG 0.004 0.000 ARG A 645 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 194 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6389 (mtt) cc_final: 0.5340 (mtt) REVERT: A 351 LEU cc_start: 0.6933 (tp) cc_final: 0.6675 (tp) REVERT: A 485 MET cc_start: 0.4124 (mmm) cc_final: 0.2375 (mtt) REVERT: A 611 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8311 (m) REVERT: A 698 MET cc_start: 0.7052 (tpp) cc_final: 0.6704 (tpp) REVERT: B 493 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5480 (m-10) REVERT: B 591 GLU cc_start: 0.6532 (pp20) cc_final: 0.6011 (pp20) REVERT: B 702 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7238 (ptp) REVERT: B 708 LEU cc_start: 0.7637 (tt) cc_final: 0.7395 (mp) REVERT: C 262 VAL cc_start: 0.5794 (OUTLIER) cc_final: 0.5587 (t) REVERT: D 258 MET cc_start: 0.2822 (mmt) cc_final: 0.2264 (mmm) REVERT: D 666 HIS cc_start: 0.5027 (OUTLIER) cc_final: 0.4738 (m-70) outliers start: 38 outliers final: 28 residues processed: 223 average time/residue: 0.2880 time to fit residues: 96.6953 Evaluate side-chains 216 residues out of total 1772 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 183 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 493 TYR Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain B residue 738 ASP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 707 SER Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain D residue 535 THR Chi-restraints excluded: chain D residue 666 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 155 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 HIS ** C 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.163210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.134977 restraints weight = 40368.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.134387 restraints weight = 30052.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.135559 restraints weight = 25603.988| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16971 Z= 0.170 Angle : 0.631 10.320 23019 Z= 0.298 Chirality : 0.044 0.156 2616 Planarity : 0.004 0.057 2975 Dihedral : 6.909 149.463 2357 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.20 % Allowed : 18.74 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.17 (0.19), residues: 2120 helix: 0.55 (0.19), residues: 844 sheet: -1.94 (0.31), residues: 256 loop : -1.60 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 563 HIS 0.007 0.001 HIS C 726 PHE 0.027 0.002 PHE A 657 TYR 0.021 0.001 TYR A 320 ARG 0.006 0.000 ARG A 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.06 seconds wall clock time: 62 minutes 22.27 seconds (3742.27 seconds total)