Starting phenix.real_space_refine on Tue Jul 29 01:36:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcx_36168/07_2025/8jcx_36168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcx_36168/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcx_36168/07_2025/8jcx_36168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcx_36168/07_2025/8jcx_36168.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcx_36168/07_2025/8jcx_36168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcx_36168/07_2025/8jcx_36168.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.040 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 16} 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: {'GLN:plan1': 5, 'ARG:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 14, 'GLU:plan': 13, 'ASP:plan': 7} 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: 7.34, per 1000 atoms: 0.69 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: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.37 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: 3.68 Time building geometry restraints manager: 3.09 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 45.720 ------------------------------------------------------------------------------- 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 : 5.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.029 0.001 TRP 2 487 HIS 0.005 0.000 HIS 2 396 PHE 0.009 0.001 PHE 2 189 TYR 0.010 0.001 TYR 2 458 ARG 0.004 0.000 ARG 2 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 0.75792 ( 6) hydrogen bonds : bond 0.14847 ( 528) hydrogen bonds : angle 5.47194 ( 1563) SS BOND : bond 0.00153 ( 18) SS BOND : angle 0.42949 ( 36) covalent geometry : bond 0.00346 (10842) covalent geometry : angle 0.53227 (14835) *********************** 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 : 1.369 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: 1.1427 time to fit residues: 162.1004 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 : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.0270 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 118 optimal weight: 1.9990 chunk 45 optimal weight: 0.0030 chunk 71 optimal weight: 40.0000 chunk 88 optimal weight: 0.5980 chunk 137 optimal weight: 20.0000 overall best weight: 0.6650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 268 ASN 3 345 ASN 3 470 ASN 3 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.227832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.143110 restraints weight = 11040.843| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.06 r_work: 0.3294 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10862 Z= 0.156 Angle : 0.532 8.037 14877 Z= 0.270 Chirality : 0.043 0.196 1720 Planarity : 0.004 0.056 1957 Dihedral : 4.255 56.351 1698 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.75 % Allowed : 8.44 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1498 helix: 2.54 (0.20), residues: 645 sheet: -1.74 (0.43), residues: 150 loop : -1.64 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 3 529 HIS 0.002 0.001 HIS 3 485 PHE 0.013 0.002 PHE 2 67 TYR 0.014 0.001 TYR 2 473 ARG 0.007 0.001 ARG 2 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00086 ( 2) link_NAG-ASN : angle 0.98380 ( 6) hydrogen bonds : bond 0.03772 ( 528) hydrogen bonds : angle 4.12407 ( 1563) SS BOND : bond 0.00200 ( 18) SS BOND : angle 0.51625 ( 36) covalent geometry : bond 0.00370 (10842) covalent geometry : angle 0.53145 (14835) *********************** 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: 16 poor density : 107 time to evaluate : 3.494 Fit side-chains REVERT: 3 63 ASP cc_start: 0.8281 (m-30) cc_final: 0.8034 (m-30) REVERT: 3 199 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7826 (mtpp) REVERT: 3 245 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: 3 508 GLN cc_start: 0.7565 (tt0) cc_final: 0.6615 (pt0) outliers start: 16 outliers final: 3 residues processed: 115 average time/residue: 1.7327 time to fit residues: 226.1022 Evaluate side-chains 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 97 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 85 optimal weight: 0.5980 chunk 72 optimal weight: 40.0000 chunk 124 optimal weight: 0.0980 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 45 optimal weight: 0.3980 chunk 86 optimal weight: 0.5980 chunk 105 optimal weight: 0.0010 chunk 80 optimal weight: 0.5980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 156 GLN 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.230916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145080 restraints weight = 11298.115| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.01 r_work: 0.3319 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10862 Z= 0.105 Angle : 0.466 7.505 14877 Z= 0.237 Chirality : 0.041 0.193 1720 Planarity : 0.003 0.058 1957 Dihedral : 4.010 52.944 1698 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.75 % Allowed : 11.40 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1498 helix: 2.58 (0.20), residues: 655 sheet: -1.56 (0.43), residues: 150 loop : -1.60 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.001 0.000 HIS 2 393 PHE 0.019 0.001 PHE 2 189 TYR 0.015 0.001 TYR 3 434 ARG 0.004 0.000 ARG 2 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.00447 ( 6) hydrogen bonds : bond 0.03193 ( 528) hydrogen bonds : angle 3.78025 ( 1563) SS BOND : bond 0.00146 ( 18) SS BOND : angle 0.42095 ( 36) covalent geometry : bond 0.00244 (10842) covalent geometry : angle 0.46533 (14835) *********************** 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 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 1.563 Fit side-chains REVERT: 2 240 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7664 (mppt) REVERT: 2 416 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7485 (ttp80) REVERT: 3 63 ASP cc_start: 0.8225 (m-30) cc_final: 0.7988 (m-30) REVERT: 3 508 GLN cc_start: 0.7641 (tt0) cc_final: 0.6703 (pt0) outliers start: 16 outliers final: 5 residues processed: 116 average time/residue: 0.9239 time to fit residues: 119.8673 Evaluate side-chains 107 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 422 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 77 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 0.4980 chunk 49 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 0.3980 chunk 75 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 268 ASN 3 345 ASN 3 470 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.226690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135703 restraints weight = 11085.180| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.95 r_work: 0.3206 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- 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: 7 | |-----------------------------------------------------------------------------| |-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: 7 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10862 Z= 0.154 Angle : 0.513 6.877 14877 Z= 0.261 Chirality : 0.043 0.226 1720 Planarity : 0.003 0.056 1957 Dihedral : 4.280 59.676 1698 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.52 % Allowed : 12.72 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1498 helix: 2.49 (0.20), residues: 657 sheet: -1.71 (0.41), residues: 160 loop : -1.58 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 56 PHE 0.013 0.001 PHE 2 67 TYR 0.015 0.001 TYR 3 434 ARG 0.006 0.000 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00022 ( 2) link_NAG-ASN : angle 1.14436 ( 6) hydrogen bonds : bond 0.03434 ( 528) hydrogen bonds : angle 3.78279 ( 1563) SS BOND : bond 0.00194 ( 18) SS BOND : angle 0.53835 ( 36) covalent geometry : bond 0.00364 (10842) covalent geometry : angle 0.51203 (14835) *********************** 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 127 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 1.142 Fit side-chains REVERT: 3 63 ASP cc_start: 0.8279 (m-30) cc_final: 0.8060 (m-30) REVERT: 3 111 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: 3 216 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8045 (t) REVERT: 3 387 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.6523 (tm-30) REVERT: 3 508 GLN cc_start: 0.7699 (tt0) cc_final: 0.6817 (pt0) outliers start: 23 outliers final: 9 residues processed: 116 average time/residue: 0.8337 time to fit residues: 108.3064 Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 352 ARG 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 216 VAL Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 504 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 144 optimal weight: 0.1980 chunk 114 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 123 optimal weight: 0.3980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 48 ASN 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.225429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.167695 restraints weight = 11022.938| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.51 r_work: 0.3490 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10862 Z= 0.149 Angle : 0.503 8.446 14877 Z= 0.256 Chirality : 0.042 0.207 1720 Planarity : 0.003 0.053 1957 Dihedral : 4.225 54.942 1698 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.52 % Allowed : 13.60 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1498 helix: 2.48 (0.20), residues: 657 sheet: -1.65 (0.40), residues: 169 loop : -1.56 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 3 529 HIS 0.002 0.001 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.016 0.001 TYR 3 434 ARG 0.004 0.000 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00062 ( 2) link_NAG-ASN : angle 1.16364 ( 6) hydrogen bonds : bond 0.03291 ( 528) hydrogen bonds : angle 3.74288 ( 1563) SS BOND : bond 0.00209 ( 18) SS BOND : angle 0.51836 ( 36) covalent geometry : bond 0.00354 (10842) covalent geometry : angle 0.50299 (14835) *********************** 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 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7801 (mppt) REVERT: 2 410 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6875 (ttt) REVERT: 2 416 ARG cc_start: 0.8024 (tpp80) cc_final: 0.7414 (ttp80) REVERT: 3 63 ASP cc_start: 0.8190 (m-30) cc_final: 0.7967 (m-30) REVERT: 3 387 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: 3 508 GLN cc_start: 0.7809 (tt0) cc_final: 0.7571 (tp40) outliers start: 23 outliers final: 10 residues processed: 114 average time/residue: 0.8231 time to fit residues: 105.6864 Evaluate side-chains 109 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP 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 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 141 LEU 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 504 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.224627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.132626 restraints weight = 11128.011| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.02 r_work: 0.3126 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3129 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10862 Z= 0.188 Angle : 0.539 7.818 14877 Z= 0.273 Chirality : 0.044 0.219 1720 Planarity : 0.003 0.051 1957 Dihedral : 4.431 57.654 1698 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.96 % Allowed : 14.47 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1498 helix: 2.41 (0.20), residues: 657 sheet: -1.73 (0.41), residues: 159 loop : -1.55 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 3 529 HIS 0.002 0.001 HIS 3 485 PHE 0.016 0.002 PHE 2 189 TYR 0.016 0.002 TYR 3 434 ARG 0.003 0.000 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.26338 ( 6) hydrogen bonds : bond 0.03509 ( 528) hydrogen bonds : angle 3.78446 ( 1563) SS BOND : bond 0.00259 ( 18) SS BOND : angle 0.59834 ( 36) covalent geometry : bond 0.00448 (10842) covalent geometry : angle 0.53803 (14835) *********************** 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 125 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7844 (mppt) REVERT: 2 375 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: 2 410 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6774 (ttt) REVERT: 2 416 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7480 (ttp80) REVERT: 2 440 GLU cc_start: 0.8261 (tp30) cc_final: 0.7955 (tt0) REVERT: 3 63 ASP cc_start: 0.8330 (m-30) cc_final: 0.8130 (m-30) REVERT: 3 245 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: 3 311 LYS cc_start: 0.7432 (ptpt) cc_final: 0.7134 (mmtt) REVERT: 3 387 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: 3 508 GLN cc_start: 0.7872 (tt0) cc_final: 0.7045 (pt0) outliers start: 27 outliers final: 11 residues processed: 115 average time/residue: 0.8877 time to fit residues: 113.4948 Evaluate side-chains 108 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 410 MET Chi-restraints excluded: chain 2 residue 482 THR 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 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 504 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 150 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 136 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.220427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139349 restraints weight = 11192.455| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.32 r_work: 0.3220 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 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 = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 10862 Z= 0.307 Angle : 0.648 9.170 14877 Z= 0.328 Chirality : 0.048 0.229 1720 Planarity : 0.004 0.050 1957 Dihedral : 5.156 56.905 1698 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.07 % Allowed : 15.13 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1498 helix: 2.19 (0.20), residues: 656 sheet: -1.89 (0.41), residues: 159 loop : -1.67 (0.23), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 3 529 HIS 0.003 0.001 HIS 3 402 PHE 0.015 0.002 PHE 2 67 TYR 0.023 0.002 TYR 3 434 ARG 0.006 0.001 ARG 3 189 Details of bonding type rmsd link_NAG-ASN : bond 0.00370 ( 2) link_NAG-ASN : angle 1.54843 ( 6) hydrogen bonds : bond 0.04148 ( 528) hydrogen bonds : angle 4.01803 ( 1563) SS BOND : bond 0.00381 ( 18) SS BOND : angle 0.75253 ( 36) covalent geometry : bond 0.00735 (10842) covalent geometry : angle 0.64754 (14835) *********************** 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 122 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.7865 (mppt) REVERT: 2 375 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.6957 (tm-30) REVERT: 3 245 GLU cc_start: 0.7518 (pm20) cc_final: 0.7089 (pm20) REVERT: 3 275 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8609 (t80) REVERT: 3 387 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: 3 508 GLN cc_start: 0.7974 (tt0) cc_final: 0.7201 (pt0) outliers start: 28 outliers final: 13 residues processed: 114 average time/residue: 0.9258 time to fit residues: 116.9365 Evaluate side-chains 109 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP 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 482 THR 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 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 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.222766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134240 restraints weight = 11004.896| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.55 r_work: 0.3255 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10862 Z= 0.170 Angle : 0.539 9.949 14877 Z= 0.274 Chirality : 0.043 0.243 1720 Planarity : 0.003 0.050 1957 Dihedral : 4.781 52.110 1698 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.07 % Allowed : 15.35 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1498 helix: 2.29 (0.20), residues: 658 sheet: -1.85 (0.41), residues: 159 loop : -1.61 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 PHE 0.013 0.002 PHE 2 67 TYR 0.018 0.002 TYR 3 434 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00074 ( 2) link_NAG-ASN : angle 1.37650 ( 6) hydrogen bonds : bond 0.03406 ( 528) hydrogen bonds : angle 3.85091 ( 1563) SS BOND : bond 0.00267 ( 18) SS BOND : angle 0.57893 ( 36) covalent geometry : bond 0.00407 (10842) covalent geometry : angle 0.53837 (14835) *********************** 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 122 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.7760 (mppt) REVERT: 2 375 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: 2 388 MET cc_start: 0.8737 (tpt) cc_final: 0.8535 (tpt) REVERT: 2 410 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: 2 416 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7541 (ttp80) REVERT: 3 245 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: 3 275 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8583 (t80) REVERT: 3 387 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: 3 508 GLN cc_start: 0.7876 (tt0) cc_final: 0.7004 (pt0) outliers start: 28 outliers final: 14 residues processed: 113 average time/residue: 0.9855 time to fit residues: 123.3060 Evaluate side-chains 111 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 410 MET Chi-restraints excluded: chain 2 residue 427 LYS Chi-restraints excluded: chain 2 residue 482 THR 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 245 GLU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 279 ASP Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 126 optimal weight: 0.0170 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.224558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.181837 restraints weight = 11156.006| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 1.55 r_work: 0.3468 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 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 = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10862 Z= 0.134 Angle : 0.516 10.774 14877 Z= 0.260 Chirality : 0.042 0.257 1720 Planarity : 0.003 0.049 1957 Dihedral : 4.553 44.364 1698 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.52 % Allowed : 16.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.23), residues: 1498 helix: 2.41 (0.20), residues: 657 sheet: -1.86 (0.40), residues: 164 loop : -1.54 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.015 0.001 TYR 2 473 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 1.34626 ( 6) hydrogen bonds : bond 0.03159 ( 528) hydrogen bonds : angle 3.73584 ( 1563) SS BOND : bond 0.00220 ( 18) SS BOND : angle 0.50971 ( 36) covalent geometry : bond 0.00318 (10842) covalent geometry : angle 0.51500 (14835) *********************** 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 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7703 (mppt) REVERT: 2 375 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6671 (tm-30) REVERT: 2 410 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.6849 (ttt) REVERT: 2 416 ARG cc_start: 0.8015 (tpp80) cc_final: 0.7544 (ttp80) REVERT: 3 245 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7065 (pm20) REVERT: 3 275 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8648 (t80) REVERT: 3 387 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: 3 508 GLN cc_start: 0.7790 (tt0) cc_final: 0.6909 (pt0) outliers start: 23 outliers final: 11 residues processed: 116 average time/residue: 0.9580 time to fit residues: 123.4578 Evaluate side-chains 115 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 410 MET Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU 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 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 387 GLU 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 79 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 94 optimal weight: 0.0030 chunk 118 optimal weight: 0.7980 chunk 70 optimal weight: 30.0000 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 127 optimal weight: 0.0770 overall best weight: 0.4748 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.226546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139291 restraints weight = 11158.087| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.22 r_work: 0.3211 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- 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: 8 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10862 Z= 0.124 Angle : 0.506 11.409 14877 Z= 0.256 Chirality : 0.042 0.243 1720 Planarity : 0.003 0.049 1957 Dihedral : 4.427 41.608 1698 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.30 % Allowed : 16.34 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1498 helix: 2.48 (0.20), residues: 657 sheet: -1.80 (0.40), residues: 164 loop : -1.51 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 PHE 0.014 0.001 PHE 3 195 TYR 0.015 0.001 TYR 2 473 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00020 ( 2) link_NAG-ASN : angle 1.30345 ( 6) hydrogen bonds : bond 0.03095 ( 528) hydrogen bonds : angle 3.67969 ( 1563) SS BOND : bond 0.00207 ( 18) SS BOND : angle 0.48500 ( 36) covalent geometry : bond 0.00294 (10842) covalent geometry : angle 0.50567 (14835) ********************** 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 118 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7682 (mppt) REVERT: 2 375 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.6728 (tm-30) REVERT: 2 410 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6655 (ttt) REVERT: 2 416 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7485 (ttp80) REVERT: 3 245 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7088 (pm20) REVERT: 3 275 PHE cc_start: 0.8959 (OUTLIER) cc_final: 0.8639 (t80) REVERT: 3 508 GLN cc_start: 0.7780 (tt0) cc_final: 0.6838 (pt0) outliers start: 21 outliers final: 11 residues processed: 113 average time/residue: 0.9078 time to fit residues: 113.7658 Evaluate side-chains 113 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 179 ASP 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 410 MET Chi-restraints excluded: chain 2 residue 482 THR Chi-restraints excluded: chain 2 residue 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU 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 279 ASP Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 504 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.1980 chunk 102 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 132 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.2578 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.226217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147269 restraints weight = 11022.826| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.20 r_work: 0.3244 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10862 Z= 0.097 Angle : 0.479 10.968 14877 Z= 0.243 Chirality : 0.041 0.245 1720 Planarity : 0.003 0.048 1957 Dihedral : 4.132 49.456 1698 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.64 % Allowed : 16.78 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1498 helix: 2.57 (0.20), residues: 659 sheet: -1.73 (0.41), residues: 164 loop : -1.45 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 315 PHE 0.013 0.001 PHE 3 195 TYR 0.015 0.001 TYR 2 473 ARG 0.004 0.000 ARG 3 270 Details of bonding type rmsd link_NAG-ASN : bond 0.00105 ( 2) link_NAG-ASN : angle 1.22163 ( 6) hydrogen bonds : bond 0.02807 ( 528) hydrogen bonds : angle 3.57412 ( 1563) SS BOND : bond 0.00173 ( 18) SS BOND : angle 0.42218 ( 36) covalent geometry : bond 0.00226 (10842) covalent geometry : angle 0.47882 (14835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8986.66 seconds wall clock time: 158 minutes 24.90 seconds (9504.90 seconds total)