Starting phenix.real_space_refine on Tue May 13 18:48:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcx_36168/05_2025/8jcx_36168.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcx_36168/05_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_36168/05_2025/8jcx_36168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcx_36168/05_2025/8jcx_36168.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcx_36168/05_2025/8jcx_36168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcx_36168/05_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-5687/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: 6.75, per 1000 atoms: 0.64 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: 2.59 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: 1.30 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: 3.21 Time building geometry restraints manager: 3.04 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: 2.840 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.300 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.930 ------------------------------------------------------------------------------- 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 : 1.046 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: 1.0466 time to fit residues: 148.8025 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 : 1.153 ------------------------------------------------------------------------------- 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 = 0.227808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.141346 restraints weight = 11040.037| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.86 r_work: 0.3309 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10862 Z= 0.157 Angle : 0.532 7.887 14877 Z= 0.270 Chirality : 0.043 0.203 1720 Planarity : 0.004 0.055 1957 Dihedral : 4.250 55.210 1698 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.86 % Allowed : 8.22 % Favored : 89.91 % 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: 2.54 (0.20), residues: 645 sheet: -1.72 (0.43), residues: 150 loop : -1.64 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 487 HIS 0.002 0.001 HIS 3 485 PHE 0.012 0.001 PHE 2 67 TYR 0.013 0.001 TYR 2 473 ARG 0.006 0.000 ARG 2 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 2) link_NAG-ASN : angle 0.97925 ( 6) hydrogen bonds : bond 0.03769 ( 528) hydrogen bonds : angle 4.11883 ( 1563) SS BOND : bond 0.00250 ( 18) SS BOND : angle 0.52311 ( 36) covalent geometry : bond 0.00371 (10842) covalent geometry : angle 0.53199 (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 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 1.079 Fit side-chains REVERT: 3 63 ASP cc_start: 0.8256 (m-30) cc_final: 0.8008 (m-30) REVERT: 3 199 LYS cc_start: 0.8340 (ttpt) cc_final: 0.7846 (mtpp) REVERT: 3 245 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6930 (pm20) REVERT: 3 508 GLN cc_start: 0.7649 (tt0) cc_final: 0.6702 (pt0) outliers start: 17 outliers final: 4 residues processed: 116 average time/residue: 0.8626 time to fit residues: 111.3953 Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 3 residue 419 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 85 optimal weight: 0.0470 chunk 72 optimal weight: 40.0000 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 chunk 37 optimal weight: 0.1980 chunk 135 optimal weight: 7.9990 chunk 45 optimal weight: 0.0050 chunk 86 optimal weight: 0.5980 chunk 105 optimal weight: 0.0270 chunk 80 optimal weight: 0.5980 overall best weight: 0.1750 ------------------------------------------------------------------------------- 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 = 0.4542 r_free = 0.4542 target = 0.232422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144955 restraints weight = 11333.825| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.30 r_work: 0.3285 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1505 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= 0.091 Angle : 0.454 7.339 14877 Z= 0.232 Chirality : 0.041 0.188 1720 Planarity : 0.003 0.058 1957 Dihedral : 3.950 50.022 1698 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.54 % Allowed : 11.40 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1498 helix: 2.64 (0.20), residues: 654 sheet: -1.54 (0.42), residues: 159 loop : -1.58 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 3 529 HIS 0.001 0.000 HIS 2 41 PHE 0.018 0.001 PHE 2 189 TYR 0.014 0.001 TYR 3 434 ARG 0.004 0.000 ARG 2 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 0.94962 ( 6) hydrogen bonds : bond 0.03074 ( 528) hydrogen bonds : angle 3.77804 ( 1563) SS BOND : bond 0.00133 ( 18) SS BOND : angle 0.39032 ( 36) covalent geometry : bond 0.00209 (10842) covalent geometry : angle 0.45414 (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 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.336 Fit side-chains REVERT: 2 27 THR cc_start: 0.8730 (m) cc_final: 0.8335 (p) REVERT: 2 240 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.7691 (mppt) REVERT: 2 374 GLN cc_start: 0.8084 (mt0) cc_final: 0.7687 (mt0) REVERT: 2 416 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7472 (ttp80) REVERT: 2 481 ASP cc_start: 0.8162 (m-30) cc_final: 0.6966 (p0) REVERT: 3 63 ASP cc_start: 0.8288 (m-30) cc_final: 0.8067 (m-30) REVERT: 3 245 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: 3 508 GLN cc_start: 0.7670 (tt0) cc_final: 0.6671 (pt0) outliers start: 14 outliers final: 5 residues processed: 119 average time/residue: 0.8574 time to fit residues: 113.3542 Evaluate side-chains 109 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 102 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 245 GLU Chi-restraints excluded: chain 3 residue 279 ASP 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: 0.9980 chunk 10 optimal weight: 0.9980 chunk 147 optimal weight: 9.9990 chunk 44 optimal weight: 0.0970 chunk 49 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 75 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.4507 r_free = 0.4507 target = 0.228200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137503 restraints weight = 11074.487| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.04 r_work: 0.3240 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10862 Z= 0.147 Angle : 0.500 6.941 14877 Z= 0.254 Chirality : 0.042 0.224 1720 Planarity : 0.003 0.056 1957 Dihedral : 4.167 57.787 1698 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.75 % Allowed : 12.94 % Favored : 85.31 % 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: 0.44 (0.23), residues: 1498 helix: 2.55 (0.20), residues: 657 sheet: -1.59 (0.43), residues: 150 loop : -1.60 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 3 529 HIS 0.002 0.000 HIS 2 393 PHE 0.012 0.001 PHE 2 67 TYR 0.014 0.001 TYR 2 473 ARG 0.003 0.000 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 2) link_NAG-ASN : angle 1.07922 ( 6) hydrogen bonds : bond 0.03333 ( 528) hydrogen bonds : angle 3.75668 ( 1563) SS BOND : bond 0.00180 ( 18) SS BOND : angle 0.49309 ( 36) covalent geometry : bond 0.00349 (10842) covalent geometry : angle 0.49970 (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 116 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.010 Fit side-chains REVERT: 2 410 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6773 (ttt) REVERT: 3 63 ASP cc_start: 0.8315 (m-30) cc_final: 0.8071 (m-30) REVERT: 3 199 LYS cc_start: 0.8347 (ttpt) cc_final: 0.7863 (mtpp) REVERT: 3 245 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: 3 508 GLN cc_start: 0.7664 (tt0) cc_final: 0.6774 (pt0) outliers start: 16 outliers final: 7 residues processed: 108 average time/residue: 0.7764 time to fit residues: 94.2641 Evaluate side-chains 108 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 209 THR 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 227 ILE Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 346 HIS Chi-restraints excluded: chain 3 residue 422 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.222961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142047 restraints weight = 11015.771| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.34 r_work: 0.3275 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10862 Z= 0.240 Angle : 0.584 8.676 14877 Z= 0.297 Chirality : 0.046 0.247 1720 Planarity : 0.004 0.055 1957 Dihedral : 4.675 59.370 1698 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.30 % Allowed : 13.49 % Favored : 84.21 % 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: 0.25 (0.22), residues: 1498 helix: 2.34 (0.20), residues: 656 sheet: -1.76 (0.42), residues: 150 loop : -1.64 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP 3 529 HIS 0.003 0.001 HIS 2 393 PHE 0.016 0.002 PHE 2 189 TYR 0.014 0.002 TYR 2 473 ARG 0.005 0.001 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 2) link_NAG-ASN : angle 1.31515 ( 6) hydrogen bonds : bond 0.03846 ( 528) hydrogen bonds : angle 3.91359 ( 1563) SS BOND : bond 0.00296 ( 18) SS BOND : angle 0.71536 ( 36) covalent geometry : bond 0.00575 (10842) covalent geometry : angle 0.58310 (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 119 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.7888 (mppt) REVERT: 2 416 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7563 (ttp80) REVERT: 2 487 TRP cc_start: 0.7121 (t60) cc_final: 0.6875 (t-100) REVERT: 3 63 ASP cc_start: 0.8227 (m-30) cc_final: 0.8014 (m-30) REVERT: 3 245 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6983 (pm20) REVERT: 3 387 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: 3 508 GLN cc_start: 0.7851 (tt0) cc_final: 0.7111 (pt0) outliers start: 21 outliers final: 8 residues processed: 109 average time/residue: 0.8794 time to fit residues: 107.3292 Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 258 LEU 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 211 THR Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 276 MET 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: 0.9980 chunk 43 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 53 optimal weight: 20.0000 chunk 118 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4469 r_free = 0.4469 target = 0.223704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138102 restraints weight = 11016.734| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 3.07 r_work: 0.3204 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10862 Z= 0.180 Angle : 0.535 9.345 14877 Z= 0.271 Chirality : 0.043 0.211 1720 Planarity : 0.003 0.053 1957 Dihedral : 4.583 59.576 1698 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.19 % Allowed : 14.91 % Favored : 82.89 % 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: 0.27 (0.22), residues: 1498 helix: 2.34 (0.20), residues: 658 sheet: -1.77 (0.41), residues: 159 loop : -1.59 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 393 PHE 0.017 0.002 PHE 2 189 TYR 0.017 0.002 TYR 3 434 ARG 0.003 0.000 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 1.28843 ( 6) hydrogen bonds : bond 0.03481 ( 528) hydrogen bonds : angle 3.84696 ( 1563) SS BOND : bond 0.00253 ( 18) SS BOND : angle 0.56644 ( 36) covalent geometry : bond 0.00429 (10842) covalent geometry : angle 0.53468 (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 118 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: 2 240 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7794 (mppt) REVERT: 2 416 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7464 (ttp80) REVERT: 3 63 ASP cc_start: 0.8235 (m-30) cc_final: 0.8035 (m-30) REVERT: 3 245 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: 3 311 LYS cc_start: 0.7264 (ptpt) cc_final: 0.6979 (mmtt) REVERT: 3 387 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.6610 (tm-30) REVERT: 3 508 GLN cc_start: 0.7815 (tt0) cc_final: 0.7024 (pt0) outliers start: 20 outliers final: 10 residues processed: 109 average time/residue: 0.8179 time to fit residues: 99.5699 Evaluate side-chains 108 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 646 CYS Chi-restraints excluded: chain 3 residue 111 GLU Chi-restraints excluded: chain 3 residue 141 LEU Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 245 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 114 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 67 optimal weight: 30.0000 chunk 150 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.219694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126690 restraints weight = 11297.112| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.12 r_work: 0.3100 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.096 10862 Z= 0.490 Angle : 0.793 12.377 14877 Z= 0.402 Chirality : 0.054 0.343 1720 Planarity : 0.005 0.054 1957 Dihedral : 6.377 63.660 1698 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.07 % Allowed : 15.24 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.28 (0.22), residues: 1498 helix: 1.84 (0.20), residues: 655 sheet: -2.05 (0.39), residues: 158 loop : -1.82 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP 3 529 HIS 0.006 0.001 HIS 2 393 PHE 0.022 0.003 PHE 3 354 TYR 0.022 0.003 TYR 3 186 ARG 0.009 0.001 ARG 2 183 Details of bonding type rmsd link_NAG-ASN : bond 0.00727 ( 2) link_NAG-ASN : angle 1.80211 ( 6) hydrogen bonds : bond 0.05012 ( 528) hydrogen bonds : angle 4.32682 ( 1563) SS BOND : bond 0.00557 ( 18) SS BOND : angle 1.01613 ( 36) covalent geometry : bond 0.01179 (10842) covalent geometry : angle 0.79128 (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 124 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.7641 (mttp) cc_final: 0.7290 (mtpm) REVERT: 2 375 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: 3 63 ASP cc_start: 0.8286 (m-30) cc_final: 0.8070 (m-30) REVERT: 3 245 GLU cc_start: 0.7666 (pm20) cc_final: 0.7133 (pm20) REVERT: 3 311 LYS cc_start: 0.7509 (ptpt) cc_final: 0.7303 (mmtt) REVERT: 3 387 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: 3 493 ASP cc_start: 0.8382 (t0) cc_final: 0.8107 (t70) REVERT: 3 508 GLN cc_start: 0.8045 (tt0) cc_final: 0.7182 (pt0) outliers start: 28 outliers final: 15 residues processed: 114 average time/residue: 0.8877 time to fit residues: 112.3154 Evaluate side-chains 113 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 65 MET Chi-restraints excluded: chain 2 residue 185 VAL Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 352 ARG Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 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 185 ASP Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 211 THR Chi-restraints excluded: chain 3 residue 387 GLU Chi-restraints excluded: chain 3 residue 419 CYS Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 527 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 66 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.223839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.136437 restraints weight = 11080.807| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 3.16 r_work: 0.3176 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10862 Z= 0.181 Angle : 0.560 11.419 14877 Z= 0.283 Chirality : 0.044 0.281 1720 Planarity : 0.004 0.053 1957 Dihedral : 5.403 55.743 1698 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.52 % Allowed : 16.12 % 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: 0.01 (0.22), residues: 1498 helix: 2.12 (0.20), residues: 659 sheet: -2.10 (0.39), residues: 164 loop : -1.68 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 3 529 HIS 0.002 0.001 HIS 3 485 PHE 0.014 0.002 PHE 2 67 TYR 0.020 0.002 TYR 3 434 ARG 0.002 0.000 ARG 3 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.46398 ( 6) hydrogen bonds : bond 0.03538 ( 528) hydrogen bonds : angle 3.97682 ( 1563) SS BOND : bond 0.00304 ( 18) SS BOND : angle 0.62912 ( 36) covalent geometry : bond 0.00431 (10842) covalent geometry : angle 0.55926 (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 123 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: 2 229 ARG cc_start: 0.7068 (mmp80) cc_final: 0.6835 (mmp-170) REVERT: 2 410 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6698 (ttt) REVERT: 2 440 GLU cc_start: 0.8487 (tt0) cc_final: 0.8147 (tt0) REVERT: 3 72 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7947 (ttt) REVERT: 3 245 GLU cc_start: 0.7582 (pm20) cc_final: 0.6976 (pm20) REVERT: 3 310 ILE cc_start: 0.6762 (pt) cc_final: 0.6418 (pt) REVERT: 3 311 LYS cc_start: 0.7430 (ptpt) cc_final: 0.7151 (mmtt) REVERT: 3 334 ASP cc_start: 0.8216 (m-30) cc_final: 0.8015 (m-30) REVERT: 3 387 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: 3 508 GLN cc_start: 0.7784 (tt0) cc_final: 0.6849 (pt0) outliers start: 23 outliers final: 12 residues processed: 115 average time/residue: 0.9158 time to fit residues: 116.5015 Evaluate side-chains 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 352 ARG 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 72 MET 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 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: 0.6980 chunk 87 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 126 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.4980 chunk 133 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.223739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129856 restraints weight = 11225.743| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.03 r_work: 0.3199 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10862 Z= 0.162 Angle : 0.549 12.390 14877 Z= 0.276 Chirality : 0.043 0.291 1720 Planarity : 0.003 0.052 1957 Dihedral : 5.113 51.426 1698 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.30 % Allowed : 16.56 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.18 (0.22), residues: 1498 helix: 2.28 (0.20), residues: 658 sheet: -1.97 (0.40), residues: 164 loop : -1.61 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.002 0.000 HIS 3 485 PHE 0.015 0.002 PHE 3 195 TYR 0.017 0.001 TYR 2 473 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00085 ( 2) link_NAG-ASN : angle 1.51260 ( 6) hydrogen bonds : bond 0.03399 ( 528) hydrogen bonds : angle 3.85885 ( 1563) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.56378 ( 36) covalent geometry : bond 0.00385 (10842) covalent geometry : angle 0.54828 (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 121 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: 2 410 MET cc_start: 0.7061 (OUTLIER) cc_final: 0.6657 (ttt) REVERT: 2 416 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7517 (ttp80) REVERT: 2 440 GLU cc_start: 0.8484 (tt0) cc_final: 0.8167 (tt0) REVERT: 3 245 GLU cc_start: 0.7640 (pm20) cc_final: 0.7046 (pm20) REVERT: 3 275 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8617 (t80) REVERT: 3 310 ILE cc_start: 0.7012 (pt) cc_final: 0.6651 (pt) REVERT: 3 387 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.6626 (tm-30) REVERT: 3 508 GLN cc_start: 0.7789 (tt0) cc_final: 0.6829 (pt0) outliers start: 21 outliers final: 12 residues processed: 114 average time/residue: 0.9351 time to fit residues: 118.2340 Evaluate side-chains 114 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 209 THR Chi-restraints excluded: chain 2 residue 352 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 79 optimal weight: 0.8980 chunk 80 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 143 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 = 0.4484 r_free = 0.4484 target = 0.225565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.136662 restraints weight = 11163.684| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 3.21 r_work: 0.3160 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10862 Z= 0.162 Angle : 0.552 13.729 14877 Z= 0.277 Chirality : 0.043 0.305 1720 Planarity : 0.003 0.052 1957 Dihedral : 5.019 51.552 1698 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.97 % Allowed : 16.78 % 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: 0.22 (0.23), residues: 1498 helix: 2.34 (0.20), residues: 657 sheet: -1.94 (0.40), residues: 164 loop : -1.62 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 3 529 HIS 0.002 0.000 HIS 3 485 PHE 0.029 0.002 PHE 3 195 TYR 0.019 0.001 TYR 3 434 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 2) link_NAG-ASN : angle 1.48021 ( 6) hydrogen bonds : bond 0.03378 ( 528) hydrogen bonds : angle 3.82745 ( 1563) SS BOND : bond 0.00258 ( 18) SS BOND : angle 0.56223 ( 36) covalent geometry : bond 0.00387 (10842) covalent geometry : angle 0.55082 (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: 18 poor density : 100 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: 2 410 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6620 (ttt) REVERT: 2 416 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7537 (ttp80) REVERT: 2 440 GLU cc_start: 0.8505 (tt0) cc_final: 0.8220 (tt0) REVERT: 3 245 GLU cc_start: 0.7701 (pm20) cc_final: 0.7095 (pm20) REVERT: 3 275 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.8633 (t80) REVERT: 3 334 ASP cc_start: 0.8127 (m-30) cc_final: 0.7650 (m-30) REVERT: 3 387 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: 3 508 GLN cc_start: 0.7841 (tt0) cc_final: 0.6891 (pt0) outliers start: 18 outliers final: 12 residues processed: 112 average time/residue: 0.9175 time to fit residues: 113.8599 Evaluate side-chains 114 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 139 VAL Chi-restraints excluded: chain 2 residue 352 ARG 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 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 36 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.0670 chunk 132 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 0.0270 chunk 12 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.225131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167405 restraints weight = 10976.606| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.55 r_work: 0.3494 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10862 Z= 0.119 Angle : 0.519 13.941 14877 Z= 0.262 Chirality : 0.042 0.289 1720 Planarity : 0.003 0.051 1957 Dihedral : 4.643 42.054 1698 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.19 % Allowed : 16.56 % 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: 0.36 (0.23), residues: 1498 helix: 2.46 (0.20), residues: 658 sheet: -1.85 (0.40), residues: 164 loop : -1.56 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 PHE 0.020 0.001 PHE 3 195 TYR 0.017 0.001 TYR 2 473 ARG 0.004 0.000 ARG 2 416 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 1.36706 ( 6) hydrogen bonds : bond 0.03043 ( 528) hydrogen bonds : angle 3.70762 ( 1563) SS BOND : bond 0.00202 ( 18) SS BOND : angle 0.48022 ( 36) covalent geometry : bond 0.00281 (10842) covalent geometry : angle 0.51850 (14835) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7910.15 seconds wall clock time: 136 minutes 31.07 seconds (8191.07 seconds total)