Starting phenix.real_space_refine on Sat Oct 11 02:20:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcx_36168/10_2025/8jcx_36168.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.040 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 6674 2.51 5 N 1880 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10617 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5251 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 37, 'TRANS': 723} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 701 Unresolved non-hydrogen angles: 902 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 8, 'ARG:plan': 16, 'ASN:plan1': 5, 'GLN:plan1': 7, 'TRP:plan': 3, 'TYR:plan': 11, 'PHE:plan': 12} Unresolved non-hydrogen planarities: 387 Chain: "3" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5286 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 29, 'TRANS': 721} Chain breaks: 3 Unresolved non-hydrogen bonds: 692 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 574 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 13, 'ASN:plan1': 10, 'ARG:plan': 13, 'GLN:plan1': 5, 'HIS:plan': 2, 'ASP:plan': 7, 'PHE:plan': 14, 'TYR:plan': 10, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 357 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.10, per 1000 atoms: 0.29 Number of scatterers: 10617 At special positions: 0 Unit cell: (86.751, 123.165, 183.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 2002 8.00 N 1880 7.00 C 6674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG 21101 " - " ASN 2 203 " " NAG 31001 " - " ASN 3 209 " Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 670.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 47.9% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain '2' and resid 59 through 74 Processing helix chain '2' and resid 94 through 110 removed outlier: 4.051A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER 2 109 " --> pdb=" O PHE 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 158 removed outlier: 4.269A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 174 Processing helix chain '2' and resid 189 through 202 removed outlier: 3.644A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 230 removed outlier: 4.104A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 260 removed outlier: 4.247A pdb=" N LYS 2 260 " --> pdb=" O ALA 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 286 removed outlier: 3.886A pdb=" N ARG 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 332 removed outlier: 3.533A pdb=" N ALA 2 328 " --> pdb=" O ILE 2 324 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 377 through 400 removed outlier: 3.620A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 422 removed outlier: 3.605A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 423 through 426 removed outlier: 3.840A pdb=" N VAL 2 426 " --> pdb=" O VAL 2 423 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 423 through 426' Processing helix chain '2' and resid 482 through 485 removed outlier: 3.873A pdb=" N ILE 2 485 " --> pdb=" O THR 2 482 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 482 through 485' Processing helix chain '2' and resid 568 through 592 Processing helix chain '2' and resid 595 through 601 removed outlier: 3.516A pdb=" N ALA 2 600 " --> pdb=" O PRO 2 596 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER 2 601 " --> pdb=" O VAL 2 597 " (cutoff:3.500A) Processing helix chain '2' and resid 602 through 623 removed outlier: 3.532A pdb=" N CYS 2 606 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) Processing helix chain '2' and resid 631 through 660 removed outlier: 4.137A pdb=" N ARG 2 656 " --> pdb=" O THR 2 652 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE 2 657 " --> pdb=" O LYS 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 702 removed outlier: 3.574A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA 2 702 " --> pdb=" O LEU 2 698 " (cutoff:3.500A) Processing helix chain '2' and resid 723 through 749 removed outlier: 3.782A pdb=" N SER 2 727 " --> pdb=" O HIS 2 723 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) Processing helix chain '2' and resid 757 through 784 removed outlier: 4.002A pdb=" N PHE 2 761 " --> pdb=" O ASN 2 757 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS 2 770 " --> pdb=" O MET 2 766 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 2 771 " --> pdb=" O TYR 2 767 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 818 removed outlier: 3.861A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 2 805 " --> pdb=" O SER 2 801 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 65 through 82 Processing helix chain '3' and resid 101 through 109 Processing helix chain '3' and resid 109 through 114 removed outlier: 3.769A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 115 through 117 No H-bonds generated for 'chain '3' and resid 115 through 117' Processing helix chain '3' and resid 150 through 162 Processing helix chain '3' and resid 176 through 180 Processing helix chain '3' and resid 195 through 208 removed outlier: 3.507A pdb=" N LYS 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 234 Processing helix chain '3' and resid 235 through 238 removed outlier: 3.584A pdb=" N ASN 3 238 " --> pdb=" O ARG 3 235 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 235 through 238' Processing helix chain '3' and resid 252 through 266 removed outlier: 3.773A pdb=" N TYR 3 256 " --> pdb=" O ILE 3 252 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS 3 266 " --> pdb=" O GLU 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 290 Processing helix chain '3' and resid 330 through 339 removed outlier: 3.933A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 3 336 " --> pdb=" O GLN 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 360 Processing helix chain '3' and resid 380 through 384 removed outlier: 3.961A pdb=" N TYR 3 384 " --> pdb=" O SER 3 381 " (cutoff:3.500A) Processing helix chain '3' and resid 389 through 412 Processing helix chain '3' and resid 426 through 433 Processing helix chain '3' and resid 494 through 497 Processing helix chain '3' and resid 578 through 601 Processing helix chain '3' and resid 614 through 632 removed outlier: 3.945A pdb=" N MET 3 628 " --> pdb=" O LEU 3 624 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 665 removed outlier: 4.436A pdb=" N LEU 3 659 " --> pdb=" O CYS 3 655 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU 3 660 " --> pdb=" O TYR 3 656 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR 3 661 " --> pdb=" O SER 3 657 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 706 removed outlier: 3.528A pdb=" N ILE 3 696 " --> pdb=" O CYS 3 692 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL 3 703 " --> pdb=" O GLN 3 699 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER 3 704 " --> pdb=" O ILE 3 700 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP 3 706 " --> pdb=" O MET 3 702 " (cutoff:3.500A) Processing helix chain '3' and resid 732 through 759 removed outlier: 4.276A pdb=" N SER 3 736 " --> pdb=" O VAL 3 732 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 3 757 " --> pdb=" O VAL 3 753 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 3 758 " --> pdb=" O TYR 3 754 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 791 removed outlier: 3.716A pdb=" N LYS 3 769 " --> pdb=" O PHE 3 765 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.558A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 3.511A pdb=" N MET 3 803 " --> pdb=" O GLN 3 799 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 27 removed outlier: 6.857A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL 2 33 " --> pdb=" O GLY 2 138 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ILE 2 140 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLY 2 35 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 206 through 207 removed outlier: 3.631A pdb=" N VAL 2 207 " --> pdb=" O CYS 2 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 210 through 212 removed outlier: 6.817A pdb=" N ALA 2 211 " --> pdb=" O VAL 2 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '2' and resid 266 through 268 removed outlier: 6.192A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '2' and resid 530 through 533 removed outlier: 5.207A pdb=" N LEU 2 532 " --> pdb=" O THR 2 536 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR 2 536 " --> pdb=" O LEU 2 532 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 32 through 35 removed outlier: 6.302A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 3 44 " --> pdb=" O ILE 3 146 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 48 through 50 removed outlier: 4.739A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 240 through 246 removed outlier: 6.664A pdb=" N VAL 3 213 " --> pdb=" O ILE 3 241 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR 3 243 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR 3 215 " --> pdb=" O THR 3 243 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 320 through 325 removed outlier: 3.872A pdb=" N ALA 3 320 " --> pdb=" O PHE 3 471 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 320 through 325 removed outlier: 3.872A pdb=" N ALA 3 320 " --> pdb=" O PHE 3 471 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 440 through 441 removed outlier: 3.866A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 518 through 521 removed outlier: 3.770A pdb=" N ILE 3 532 " --> pdb=" O LYS 3 519 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET 3 521 " --> pdb=" O ILE 3 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 539 through 540 removed outlier: 3.513A pdb=" N MET 3 547 " --> pdb=" O TYR 3 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 553 through 554 533 hydrogen bonds defined for protein. 1563 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: 1.98 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3609 1.34 - 1.46: 2523 1.46 - 1.58: 4630 1.58 - 1.70: 3 1.70 - 1.81: 77 Bond restraints: 10842 Sorted by residual: bond pdb=" CAT Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" CAT Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.364 1.452 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CAS Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CAS Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.369 1.448 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" CB PRO 2 496 " pdb=" CG PRO 2 496 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.58e+00 ... (remaining 10837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 14639 1.94 - 3.87: 148 3.87 - 5.81: 36 5.81 - 7.74: 7 7.74 - 9.68: 5 Bond angle restraints: 14835 Sorted by residual: angle pdb=" CA PRO 2 496 " pdb=" N PRO 2 496 " pdb=" CD PRO 2 496 " ideal model delta sigma weight residual 112.00 104.96 7.04 1.40e+00 5.10e-01 2.53e+01 angle pdb=" CA PRO 3 267 " pdb=" N PRO 3 267 " pdb=" CD PRO 3 267 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA PRO 2 133 " pdb=" N PRO 2 133 " pdb=" CD PRO 2 133 " ideal model delta sigma weight residual 112.00 106.21 5.79 1.40e+00 5.10e-01 1.71e+01 angle pdb=" CAX Z99 31002 " pdb=" CAZ Z99 31002 " pdb=" CAY Z99 31002 " ideal model delta sigma weight residual 120.67 110.99 9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" OAC Z99 31002 " pdb=" CAR Z99 31002 " pdb=" OAE Z99 31002 " ideal model delta sigma weight residual 127.15 119.14 8.01 3.00e+00 1.11e-01 7.13e+00 ... (remaining 14830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 6397 35.99 - 71.98: 81 71.98 - 107.97: 11 107.97 - 143.96: 2 143.96 - 179.95: 2 Dihedral angle restraints: 6493 sinusoidal: 2111 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 27.53 65.47 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS 3 549 " pdb=" SG CYS 3 549 " pdb=" SG CYS 3 562 " pdb=" CB CYS 3 562 " ideal model delta sinusoidal sigma weight residual 93.00 147.49 -54.49 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual -86.00 -36.85 -49.15 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 6490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.050: 1718 1.050 - 2.100: 0 2.100 - 3.150: 0 3.150 - 4.200: 0 4.200 - 5.250: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CAW Z99 21102 " pdb=" CAN Z99 21102 " pdb=" CAU Z99 21102 " pdb=" CAV Z99 21102 " both_signs ideal model delta sigma weight residual False 2.61 -2.64 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" CAW Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAU Z99 31002 " pdb=" CAV Z99 31002 " both_signs ideal model delta sigma weight residual False 2.61 -2.52 5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" CAZ Z99 21102 " pdb=" CAO Z99 21102 " pdb=" CAX Z99 21102 " pdb=" CAY Z99 21102 " both_signs ideal model delta sigma weight residual True 2.39 -2.71 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1717 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 2 132 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO 2 133 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO 2 133 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO 2 133 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 495 " 0.052 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO 2 496 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO 2 496 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 2 496 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 3 266 " 0.034 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO 3 267 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO 3 267 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 3 267 " 0.027 5.00e-02 4.00e+02 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1710 2.76 - 3.30: 10079 3.30 - 3.83: 17815 3.83 - 4.37: 19258 4.37 - 4.90: 34367 Nonbonded interactions: 83229 Sorted by model distance: nonbonded pdb=" OE1 GLN 2 159 " pdb=" OH TYR 2 180 " model vdw 2.225 3.040 nonbonded pdb=" NH1 ARG 2 460 " pdb=" O ALA 2 461 " model vdw 2.269 3.120 nonbonded pdb=" O ILE 3 788 " pdb=" OG1 THR 3 792 " model vdw 2.271 3.040 nonbonded pdb=" NH1 ARG 3 31 " pdb=" OD2 ASP 3 353 " model vdw 2.297 3.120 nonbonded pdb=" NE1 TRP 2 204 " pdb=" O LEU 2 495 " model vdw 2.304 3.120 ... (remaining 83224 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.870 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.060 Process input model: 12.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 0.128 10862 Z= 0.143 Angle : 0.532 9.675 14877 Z= 0.259 Chirality : 0.182 5.250 1720 Planarity : 0.004 0.104 1957 Dihedral : 13.649 179.949 3601 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1498 helix: 2.58 (0.21), residues: 648 sheet: -2.03 (0.45), residues: 147 loop : -1.62 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 346 TYR 0.010 0.001 TYR 2 458 PHE 0.009 0.001 PHE 2 189 TRP 0.029 0.001 TRP 2 487 HIS 0.005 0.000 HIS 2 396 Details of bonding type rmsd covalent geometry : bond 0.00346 (10842) covalent geometry : angle 0.53227 (14835) SS BOND : bond 0.00153 ( 18) SS BOND : angle 0.42949 ( 36) hydrogen bonds : bond 0.14847 ( 528) hydrogen bonds : angle 5.47194 ( 1563) link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 0.75792 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.429 Fit side-chains REVERT: 3 63 ASP cc_start: 0.7761 (m-30) cc_final: 0.7558 (m-30) REVERT: 3 508 GLN cc_start: 0.6996 (tt0) cc_final: 0.6221 (pt0) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5354 time to fit residues: 75.5679 Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 268 ASN 3 292 ASN 3 345 ASN 3 470 ASN 3 472 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.226751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136349 restraints weight = 11282.826| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 3.42 r_work: 0.3210 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10862 Z= 0.223 Angle : 0.596 8.650 14877 Z= 0.304 Chirality : 0.045 0.235 1720 Planarity : 0.004 0.057 1957 Dihedral : 4.523 58.370 1698 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.30 % Allowed : 9.10 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1498 helix: 2.31 (0.20), residues: 649 sheet: -1.83 (0.42), residues: 150 loop : -1.71 (0.22), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 74 TYR 0.014 0.002 TYR 2 473 PHE 0.016 0.002 PHE 2 38 TRP 0.012 0.002 TRP 2 297 HIS 0.004 0.001 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00528 (10842) covalent geometry : angle 0.59537 (14835) SS BOND : bond 0.00391 ( 18) SS BOND : angle 0.68138 ( 36) hydrogen bonds : bond 0.04166 ( 528) hydrogen bonds : angle 4.18678 ( 1563) link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 1.14966 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.410 Fit side-chains REVERT: 2 395 MET cc_start: 0.8022 (ttt) cc_final: 0.7782 (ttm) REVERT: 3 63 ASP cc_start: 0.8276 (m-30) cc_final: 0.8052 (m-30) REVERT: 3 104 TYR cc_start: 0.8909 (t80) cc_final: 0.8635 (t80) REVERT: 3 199 LYS cc_start: 0.8351 (ttpt) cc_final: 0.8141 (ttmm) REVERT: 3 245 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6863 (pm20) REVERT: 3 387 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6479 (tm-30) REVERT: 3 508 GLN cc_start: 0.7659 (tt0) cc_final: 0.6754 (pt0) outliers start: 21 outliers final: 6 residues processed: 114 average time/residue: 0.4406 time to fit residues: 55.7325 Evaluate side-chains 108 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 419 CYS Chi-restraints excluded: chain 3 residue 441 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 4 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 68 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 55 optimal weight: 40.0000 chunk 7 optimal weight: 0.9990 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 48 ASN 3 156 GLN 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.223734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.134210 restraints weight = 11132.139| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.58 r_work: 0.3281 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10862 Z= 0.183 Angle : 0.538 8.579 14877 Z= 0.274 Chirality : 0.043 0.223 1720 Planarity : 0.004 0.058 1957 Dihedral : 4.410 57.445 1698 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.41 % Allowed : 12.61 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.22), residues: 1498 helix: 2.32 (0.20), residues: 657 sheet: -1.79 (0.40), residues: 169 loop : -1.66 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 74 TYR 0.016 0.002 TYR 3 434 PHE 0.018 0.002 PHE 2 189 TRP 0.020 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 393 Details of bonding type rmsd covalent geometry : bond 0.00436 (10842) covalent geometry : angle 0.53727 (14835) SS BOND : bond 0.00223 ( 18) SS BOND : angle 0.56023 ( 36) hydrogen bonds : bond 0.03725 ( 528) hydrogen bonds : angle 3.97878 ( 1563) link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 1.24009 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.451 Fit side-chains REVERT: 2 240 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.7800 (mppt) REVERT: 2 375 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.6729 (tm-30) REVERT: 2 395 MET cc_start: 0.8077 (ttt) cc_final: 0.7839 (ttm) REVERT: 2 481 ASP cc_start: 0.8111 (m-30) cc_final: 0.6901 (p0) REVERT: 3 63 ASP cc_start: 0.8166 (m-30) cc_final: 0.7958 (m-30) REVERT: 3 104 TYR cc_start: 0.8961 (t80) cc_final: 0.8702 (t80) REVERT: 3 111 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: 3 216 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8028 (t) REVERT: 3 245 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: 3 387 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.6462 (tm-30) REVERT: 3 508 GLN cc_start: 0.7686 (tt0) cc_final: 0.6854 (pt0) outliers start: 22 outliers final: 6 residues processed: 118 average time/residue: 0.4438 time to fit residues: 57.9141 Evaluate side-chains 115 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 5.9990 chunk 144 optimal weight: 0.0040 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 133 optimal weight: 30.0000 chunk 64 optimal weight: 50.0000 chunk 53 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4461 r_free = 0.4461 target = 0.223575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.132819 restraints weight = 11236.182| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.17 r_work: 0.3166 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10862 Z= 0.216 Angle : 0.568 9.690 14877 Z= 0.289 Chirality : 0.044 0.231 1720 Planarity : 0.004 0.059 1957 Dihedral : 4.597 57.642 1698 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.51 % Allowed : 13.05 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.22), residues: 1498 helix: 2.26 (0.20), residues: 655 sheet: -1.81 (0.40), residues: 169 loop : -1.68 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 189 TYR 0.019 0.002 TYR 3 434 PHE 0.015 0.002 PHE 2 67 TRP 0.020 0.001 TRP 3 529 HIS 0.002 0.001 HIS 3 402 Details of bonding type rmsd covalent geometry : bond 0.00517 (10842) covalent geometry : angle 0.56767 (14835) SS BOND : bond 0.00280 ( 18) SS BOND : angle 0.65436 ( 36) hydrogen bonds : bond 0.03798 ( 528) hydrogen bonds : angle 3.96471 ( 1563) link_NAG-ASN : bond 0.00183 ( 2) link_NAG-ASN : angle 1.32631 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.7825 (mppt) REVERT: 2 375 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: 2 416 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7488 (ttp80) REVERT: 2 481 ASP cc_start: 0.8174 (m-30) cc_final: 0.6902 (p0) REVERT: 3 63 ASP cc_start: 0.8304 (m-30) cc_final: 0.8090 (m-30) REVERT: 3 104 TYR cc_start: 0.8988 (t80) cc_final: 0.8635 (t80) REVERT: 3 245 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: 3 387 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.6607 (tm-30) REVERT: 3 508 GLN cc_start: 0.7809 (tt0) cc_final: 0.7019 (pt0) outliers start: 32 outliers final: 17 residues processed: 121 average time/residue: 0.4241 time to fit residues: 57.0734 Evaluate side-chains 115 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 419 CYS Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 26 optimal weight: 0.3980 chunk 125 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4451 r_free = 0.4451 target = 0.221965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.163128 restraints weight = 11020.550| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.56 r_work: 0.3419 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10862 Z= 0.234 Angle : 0.581 10.432 14877 Z= 0.294 Chirality : 0.045 0.227 1720 Planarity : 0.004 0.056 1957 Dihedral : 4.834 57.529 1698 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.62 % Allowed : 14.69 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.22), residues: 1498 helix: 2.20 (0.20), residues: 656 sheet: -1.83 (0.42), residues: 159 loop : -1.69 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG 2 183 TYR 0.019 0.002 TYR 3 434 PHE 0.024 0.002 PHE 2 189 TRP 0.019 0.002 TRP 3 529 HIS 0.002 0.001 HIS 2 365 Details of bonding type rmsd covalent geometry : bond 0.00563 (10842) covalent geometry : angle 0.57974 (14835) SS BOND : bond 0.00315 ( 18) SS BOND : angle 0.65817 ( 36) hydrogen bonds : bond 0.03846 ( 528) hydrogen bonds : angle 3.99290 ( 1563) link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 1.44080 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7810 (mppt) REVERT: 2 375 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: 3 63 ASP cc_start: 0.8213 (m-30) cc_final: 0.8012 (m-30) REVERT: 3 233 GLU cc_start: 0.8096 (tp30) cc_final: 0.7877 (tp30) REVERT: 3 245 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6963 (pm20) REVERT: 3 311 LYS cc_start: 0.7391 (ptpt) cc_final: 0.7154 (mmtt) REVERT: 3 387 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: 3 508 GLN cc_start: 0.7783 (tt0) cc_final: 0.6914 (pt0) outliers start: 33 outliers final: 19 residues processed: 117 average time/residue: 0.4715 time to fit residues: 60.5735 Evaluate side-chains 118 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 34 optimal weight: 0.5980 chunk 145 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4422 r_free = 0.4422 target = 0.219014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132402 restraints weight = 11118.737| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.00 r_work: 0.3125 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 10862 Z= 0.340 Angle : 0.670 11.534 14877 Z= 0.339 Chirality : 0.048 0.300 1720 Planarity : 0.004 0.055 1957 Dihedral : 5.756 54.744 1698 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.93 % Allowed : 13.82 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.22), residues: 1498 helix: 2.01 (0.20), residues: 659 sheet: -2.05 (0.39), residues: 163 loop : -1.76 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 183 TYR 0.023 0.002 TYR 3 434 PHE 0.017 0.002 PHE 2 67 TRP 0.018 0.002 TRP 3 529 HIS 0.003 0.001 HIS 3 402 Details of bonding type rmsd covalent geometry : bond 0.00820 (10842) covalent geometry : angle 0.66916 (14835) SS BOND : bond 0.00420 ( 18) SS BOND : angle 0.80598 ( 36) hydrogen bonds : bond 0.04369 ( 528) hydrogen bonds : angle 4.14871 ( 1563) link_NAG-ASN : bond 0.00416 ( 2) link_NAG-ASN : angle 1.70781 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: 2 206 TYR cc_start: 0.8310 (t80) cc_final: 0.7703 (t80) REVERT: 2 240 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.7803 (mppt) REVERT: 2 375 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: 2 410 MET cc_start: 0.7211 (OUTLIER) cc_final: 0.6851 (ttt) REVERT: 3 63 ASP cc_start: 0.8309 (m-30) cc_final: 0.8092 (m-30) REVERT: 3 245 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7128 (pm20) REVERT: 3 275 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8660 (t80) REVERT: 3 311 LYS cc_start: 0.7505 (ptpt) cc_final: 0.7291 (mmtt) REVERT: 3 387 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.6802 (tm-30) REVERT: 3 508 GLN cc_start: 0.7879 (tt0) cc_final: 0.6953 (pt0) outliers start: 45 outliers final: 23 residues processed: 129 average time/residue: 0.4771 time to fit residues: 67.5986 Evaluate side-chains 125 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 57 CYS Chi-restraints excluded: chain 3 residue 93 VAL Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 215 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 419 CYS Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 80 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 64 optimal weight: 30.0000 chunk 139 optimal weight: 0.0980 chunk 100 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 57 optimal weight: 30.0000 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 40.0000 chunk 26 optimal weight: 2.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4473 r_free = 0.4473 target = 0.224885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.133789 restraints weight = 11130.510| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.40 r_work: 0.3203 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3208 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10862 Z= 0.125 Angle : 0.516 10.311 14877 Z= 0.262 Chirality : 0.042 0.254 1720 Planarity : 0.003 0.053 1957 Dihedral : 4.838 43.205 1698 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.85 % Allowed : 16.01 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.22), residues: 1498 helix: 2.30 (0.20), residues: 657 sheet: -1.91 (0.41), residues: 164 loop : -1.63 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 416 TYR 0.017 0.001 TYR 2 473 PHE 0.014 0.001 PHE 3 195 TRP 0.023 0.001 TRP 3 529 HIS 0.002 0.000 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00293 (10842) covalent geometry : angle 0.51495 (14835) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.51919 ( 36) hydrogen bonds : bond 0.03228 ( 528) hydrogen bonds : angle 3.84383 ( 1563) link_NAG-ASN : bond 0.00030 ( 2) link_NAG-ASN : angle 1.40153 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.405 Fit side-chains REVERT: 2 240 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7700 (mppt) REVERT: 2 410 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: 2 416 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7551 (ttp80) REVERT: 2 469 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8170 (tt0) REVERT: 3 245 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: 3 275 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8670 (t80) REVERT: 3 508 GLN cc_start: 0.7665 (tt0) cc_final: 0.6665 (pt0) outliers start: 26 outliers final: 9 residues processed: 120 average time/residue: 0.4704 time to fit residues: 62.3102 Evaluate side-chains 113 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 57 CYS Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 504 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 10.0000 chunk 144 optimal weight: 0.0040 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 40.0000 chunk 121 optimal weight: 0.3980 chunk 122 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4482 r_free = 0.4482 target = 0.225369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134220 restraints weight = 11059.822| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.30 r_work: 0.3185 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10862 Z= 0.138 Angle : 0.525 10.247 14877 Z= 0.266 Chirality : 0.042 0.249 1720 Planarity : 0.003 0.052 1957 Dihedral : 4.744 42.999 1698 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.52 % Allowed : 16.67 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.23), residues: 1498 helix: 2.40 (0.20), residues: 656 sheet: -1.86 (0.41), residues: 164 loop : -1.58 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 416 TYR 0.018 0.001 TYR 2 473 PHE 0.015 0.001 PHE 3 195 TRP 0.023 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00327 (10842) covalent geometry : angle 0.52478 (14835) SS BOND : bond 0.00238 ( 18) SS BOND : angle 0.51863 ( 36) hydrogen bonds : bond 0.03256 ( 528) hydrogen bonds : angle 3.76667 ( 1563) link_NAG-ASN : bond 0.00034 ( 2) link_NAG-ASN : angle 1.41704 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.432 Fit side-chains REVERT: 2 239 GLU cc_start: 0.8107 (mp0) cc_final: 0.7682 (mm-30) REVERT: 2 240 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7705 (mppt) REVERT: 2 410 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6675 (ttt) REVERT: 2 416 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7546 (ttp80) REVERT: 2 469 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: 3 245 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: 3 275 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8596 (t80) REVERT: 3 331 ARG cc_start: 0.7780 (mmt180) cc_final: 0.6947 (mtm-85) REVERT: 3 508 GLN cc_start: 0.7781 (tt0) cc_final: 0.6779 (pt0) outliers start: 23 outliers final: 12 residues processed: 117 average time/residue: 0.4786 time to fit residues: 61.9497 Evaluate side-chains 119 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 504 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 4 optimal weight: 0.5980 chunk 85 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 10 optimal weight: 0.7980 chunk 61 optimal weight: 30.0000 chunk 0 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 342 ASN ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN 3 386 GLN ** 3 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.223930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.135134 restraints weight = 11082.514| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.12 r_work: 0.3311 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10862 Z= 0.126 Angle : 0.514 10.172 14877 Z= 0.260 Chirality : 0.042 0.233 1720 Planarity : 0.003 0.051 1957 Dihedral : 4.570 38.374 1698 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.41 % Allowed : 16.78 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.23), residues: 1498 helix: 2.47 (0.20), residues: 656 sheet: -1.81 (0.41), residues: 164 loop : -1.55 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 416 TYR 0.018 0.001 TYR 2 473 PHE 0.028 0.001 PHE 3 195 TRP 0.024 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00299 (10842) covalent geometry : angle 0.51323 (14835) SS BOND : bond 0.00220 ( 18) SS BOND : angle 0.47674 ( 36) hydrogen bonds : bond 0.03132 ( 528) hydrogen bonds : angle 3.70047 ( 1563) link_NAG-ASN : bond 0.00023 ( 2) link_NAG-ASN : angle 1.35634 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.438 Fit side-chains REVERT: 2 240 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7775 (mppt) REVERT: 2 410 MET cc_start: 0.7146 (OUTLIER) cc_final: 0.6673 (ttt) REVERT: 2 416 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7614 (ttp80) REVERT: 2 469 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8289 (tt0) REVERT: 3 245 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7067 (pm20) REVERT: 3 275 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8701 (t80) REVERT: 3 508 GLN cc_start: 0.7843 (tt0) cc_final: 0.6857 (pt0) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.4502 time to fit residues: 57.4068 Evaluate side-chains 119 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 57 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 83 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 67 optimal weight: 30.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** 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 = 0.4482 r_free = 0.4482 target = 0.225382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134135 restraints weight = 11022.507| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.32 r_work: 0.3182 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10862 Z= 0.158 Angle : 0.537 10.833 14877 Z= 0.271 Chirality : 0.043 0.249 1720 Planarity : 0.003 0.051 1957 Dihedral : 4.685 42.826 1698 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.85 % Allowed : 16.67 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.23), residues: 1498 helix: 2.43 (0.20), residues: 658 sheet: -1.86 (0.41), residues: 164 loop : -1.54 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 416 TYR 0.018 0.001 TYR 2 473 PHE 0.018 0.001 PHE 3 195 TRP 0.023 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00378 (10842) covalent geometry : angle 0.53642 (14835) SS BOND : bond 0.00241 ( 18) SS BOND : angle 0.54319 ( 36) hydrogen bonds : bond 0.03314 ( 528) hydrogen bonds : angle 3.73728 ( 1563) link_NAG-ASN : bond 0.00094 ( 2) link_NAG-ASN : angle 1.39970 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7679 (mppt) REVERT: 2 410 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6669 (ttt) REVERT: 2 416 ARG cc_start: 0.8062 (tpp80) cc_final: 0.7529 (ttp80) REVERT: 2 469 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: 3 245 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7026 (pm20) REVERT: 3 275 PHE cc_start: 0.8965 (OUTLIER) cc_final: 0.8664 (t80) REVERT: 3 334 ASP cc_start: 0.8207 (m-30) cc_final: 0.7603 (m-30) REVERT: 3 508 GLN cc_start: 0.7805 (tt0) cc_final: 0.6820 (pt0) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 0.4544 time to fit residues: 59.6140 Evaluate side-chains 120 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 191 GLN Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 469 GLN Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 57 CYS Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 146 optimal weight: 10.0000 chunk 58 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 118 optimal weight: 0.2980 chunk 28 optimal weight: 0.2980 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 342 ASN ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN ** 3 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.225255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.167214 restraints weight = 10996.389| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.50 r_work: 0.3486 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10862 Z= 0.121 Angle : 0.512 10.714 14877 Z= 0.260 Chirality : 0.042 0.247 1720 Planarity : 0.003 0.050 1957 Dihedral : 4.489 36.735 1698 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.63 % Allowed : 17.00 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.23), residues: 1498 helix: 2.49 (0.20), residues: 658 sheet: -1.76 (0.41), residues: 164 loop : -1.51 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 416 TYR 0.018 0.001 TYR 2 473 PHE 0.016 0.001 PHE 3 195 TRP 0.023 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00288 (10842) covalent geometry : angle 0.51192 (14835) SS BOND : bond 0.00210 ( 18) SS BOND : angle 0.46059 ( 36) hydrogen bonds : bond 0.03074 ( 528) hydrogen bonds : angle 3.66794 ( 1563) link_NAG-ASN : bond 0.00045 ( 2) link_NAG-ASN : angle 1.31106 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4543.09 seconds wall clock time: 77 minutes 53.89 seconds (4673.89 seconds total)