Starting phenix.real_space_refine on Sat Sep 12 02:47:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.map" model { file = "/net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pyh_20524/09_2026/6pyh_20524.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 102 5.16 5 C 8342 2.51 5 N 2285 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13187 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6360 Classifications: {'peptide': 793} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 46, 'TRANS': 744} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 416 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6411 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 754} Chain breaks: 10 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 2.53, per 1000 atoms: 0.19 Number of scatterers: 13187 At special positions: 0 Unit cell: (120.91, 113.42, 171.2, 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 102 16.00 O 2458 8.00 N 2285 7.00 C 8342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 22 " distance=2.03 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 148 " distance=2.02 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 194 " distance=2.02 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 200 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 205 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 291 " distance=2.04 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 426 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS A 671 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 777 " - pdb=" SG CYS A 786 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 48 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 61 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 22 " distance=2.02 Simple disulfide: pdb=" SG CYS D 120 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 175 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 181 " distance=2.04 Simple disulfide: pdb=" SG CYS D 185 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 200 " distance=2.04 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 221 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 234 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 273 " distance=2.04 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 324 " distance=2.03 Simple disulfide: pdb=" SG CYS D 777 " - pdb=" SG CYS D 786 " distance=2.04 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 Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 521.0 milliseconds 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 30 sheets defined 13.3% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 248 through 254 removed outlier: 4.594A pdb=" N CYS A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.767A pdb=" N ALA A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET A 320 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 350 removed outlier: 4.526A pdb=" N GLU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 373 removed outlier: 4.489A pdb=" N PHE A 372 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 438 removed outlier: 3.854A pdb=" N ILE A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLU A 435 " --> pdb=" O TYR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 702 removed outlier: 4.013A pdb=" N ALA A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 685 " --> pdb=" O GLN A 681 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 697 " --> pdb=" O PHE A 693 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 702 " --> pdb=" O HIS A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.965A pdb=" N VAL B 11 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 13 " --> pdb=" O GLU B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'D' and resid 12 through 20 Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 248 through 254 removed outlier: 3.613A pdb=" N CYS D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 340 through 350 removed outlier: 4.025A pdb=" N GLU D 344 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 373 removed outlier: 4.235A pdb=" N PHE D 372 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 428 through 437 Processing helix chain 'D' and resid 625 through 631 removed outlier: 3.966A pdb=" N TYR D 629 " --> pdb=" O ASP D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 699 removed outlier: 3.523A pdb=" N LYS D 680 " --> pdb=" O THR D 676 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N PHE D 696 " --> pdb=" O VAL D 692 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 697 " --> pdb=" O PHE D 693 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 699 " --> pdb=" O ASN D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 853 through 860 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 removed outlier: 3.534A pdb=" N THR A 52 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 11.262A pdb=" N VAL A 50 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 10.184A pdb=" N TRP A 79 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N THR A 52 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.539A pdb=" N ILE A 31 " --> pdb=" O PHE A 58 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE A 90 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 57 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 114 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N VAL A 140 " --> pdb=" O ILE A 111 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 113 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 166 removed outlier: 3.629A pdb=" N ASN A 172 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209 removed outlier: 7.098A pdb=" N SER A 208 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 284 removed outlier: 4.693A pdb=" N TYR A 290 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 5.668A pdb=" N LEU A 331 " --> pdb=" O LYS A 360 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ARG A 362 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE A 333 " --> pdb=" O ARG A 362 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 359 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N LEU A 394 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A 361 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR A 418 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR A 392 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ALA A 420 " --> pdb=" O TYR A 392 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU A 394 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 462 through 463 removed outlier: 6.425A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 568 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 555 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 493 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463 removed outlier: 6.425A pdb=" N ASP A 462 " --> pdb=" O LYS A 569 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 568 " --> pdb=" O ALA A 554 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 472 Processing sheet with id=AB4, first strand: chain 'A' and resid 586 through 594 removed outlier: 4.550A pdb=" N VAL A 588 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS A 601 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N SER A 590 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 599 " --> pdb=" O SER A 590 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N SER A 592 " --> pdb=" O GLN A 597 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN A 597 " --> pdb=" O SER A 592 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 759 " --> pdb=" O VAL A 600 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 753 removed outlier: 3.534A pdb=" N VAL A 617 " --> pdb=" O SER A 751 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN A 620 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 818 through 820 Processing sheet with id=AB7, first strand: chain 'A' and resid 847 through 852 Processing sheet with id=AB8, first strand: chain 'A' and resid 847 through 852 removed outlier: 7.136A pdb=" N THR A 879 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 2 through 3 removed outlier: 3.848A pdb=" N ILE D 76 " --> pdb=" O ASN D 105 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 6 through 10 removed outlier: 5.931A pdb=" N ILE D 7 " --> pdb=" O HIS D 30 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU D 32 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE D 9 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE D 34 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 60 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE D 90 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 57 " --> pdb=" O PHE D 90 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG D 112 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 89 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 114 " --> pdb=" O ILE D 89 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 239 through 241 Processing sheet with id=AC3, first strand: chain 'D' and resid 267 through 269 Processing sheet with id=AC4, first strand: chain 'D' and resid 281 through 284 removed outlier: 5.949A pdb=" N TYR D 290 " --> pdb=" O ASN D 284 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 311 through 312 removed outlier: 6.269A pdb=" N LEU D 331 " --> pdb=" O LYS D 360 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ARG D 362 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE D 333 " --> pdb=" O ARG D 362 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL D 359 " --> pdb=" O TYR D 392 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LEU D 394 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 361 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 354 through 355 removed outlier: 3.530A pdb=" N VAL D 355 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 379 " --> pdb=" O THR D 411 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 466 through 468 Processing sheet with id=AC8, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AC9, first strand: chain 'D' and resid 586 through 594 removed outlier: 5.630A pdb=" N ASP D 587 " --> pdb=" O ASN D 603 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN D 603 " --> pdb=" O ASP D 587 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN D 593 " --> pdb=" O GLN D 597 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLN D 597 " --> pdb=" O ASN D 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 612 through 621 Processing sheet with id=AD2, first strand: chain 'D' and resid 810 through 812 removed outlier: 3.767A pdb=" N LEU D 864 " --> pdb=" O ILE D 819 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 847 through 851 removed outlier: 3.733A pdb=" N MET D 835 " --> pdb=" O THR D 879 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 895 " --> pdb=" O GLY D 870 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 642 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: 2.60 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 13366 1.56 - 1.91: 126 1.91 - 2.25: 0 2.25 - 2.59: 0 2.59 - 2.94: 1 Bond restraints: 13493 Sorted by residual: bond pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 1.329 2.936 -1.607 1.40e-02 5.10e+03 1.32e+04 bond pdb=" C ALA A 501 " pdb=" N PRO A 502 " ideal model delta sigma weight residual 1.334 1.308 0.025 8.40e-03 1.42e+04 9.18e+00 bond pdb=" CB TRP A 405 " pdb=" CG TRP A 405 " ideal model delta sigma weight residual 1.498 1.442 0.056 3.10e-02 1.04e+03 3.21e+00 bond pdb=" C ALA D 117 " pdb=" N ASP D 118 " ideal model delta sigma weight residual 1.332 1.308 0.024 1.40e-02 5.10e+03 3.00e+00 bond pdb=" CA PRO A 144 " pdb=" C PRO A 144 " ideal model delta sigma weight residual 1.517 1.501 0.016 9.30e-03 1.16e+04 2.88e+00 ... (remaining 13488 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.83: 18295 14.83 - 29.65: 0 29.65 - 44.48: 0 44.48 - 59.30: 0 59.30 - 74.13: 1 Bond angle restraints: 18296 Sorted by residual: angle pdb=" O PRO A 798 " pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 122.89 48.76 74.13 1.25e+00 6.40e-01 3.52e+03 angle pdb=" CA PRO A 798 " pdb=" C PRO A 798 " pdb=" N ALA A 799 " ideal model delta sigma weight residual 115.12 126.49 -11.37 1.25e+00 6.40e-01 8.28e+01 angle pdb=" C PRO A 798 " pdb=" N ALA A 799 " pdb=" CA ALA A 799 " ideal model delta sigma weight residual 121.70 109.37 12.33 1.80e+00 3.09e-01 4.69e+01 angle pdb=" N GLN A 843 " pdb=" CA GLN A 843 " pdb=" C GLN A 843 " ideal model delta sigma weight residual 114.75 108.87 5.88 1.26e+00 6.30e-01 2.18e+01 angle pdb=" C MET A 184 " pdb=" N CYS A 185 " pdb=" CA CYS A 185 " ideal model delta sigma weight residual 120.94 113.03 7.91 1.90e+00 2.77e-01 1.73e+01 ... (remaining 18291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 7198 17.90 - 35.79: 806 35.79 - 53.69: 150 53.69 - 71.58: 26 71.58 - 89.48: 9 Dihedral angle restraints: 8189 sinusoidal: 3379 harmonic: 4810 Sorted by residual: dihedral pdb=" CA GLU D 816 " pdb=" C GLU D 816 " pdb=" N ASN D 817 " pdb=" CA ASN D 817 " ideal model delta harmonic sigma weight residual -180.00 -130.16 -49.84 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CB CYS D 189 " pdb=" SG CYS D 189 " pdb=" SG CYS D 200 " pdb=" CB CYS D 200 " ideal model delta sinusoidal sigma weight residual 93.00 3.52 89.48 1 1.00e+01 1.00e-02 9.51e+01 dihedral pdb=" CB CYS D 777 " pdb=" SG CYS D 777 " pdb=" SG CYS D 786 " pdb=" CB CYS D 786 " ideal model delta sinusoidal sigma weight residual -86.00 -167.98 81.98 1 1.00e+01 1.00e-02 8.26e+01 ... (remaining 8186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1125 0.036 - 0.072: 538 0.072 - 0.108: 239 0.108 - 0.143: 67 0.143 - 0.179: 9 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ILE A 575 " pdb=" N ILE A 575 " pdb=" C ILE A 575 " pdb=" CB ILE A 575 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CB ILE D 448 " pdb=" CA ILE D 448 " pdb=" CG1 ILE D 448 " pdb=" CG2 ILE D 448 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA PRO A 153 " pdb=" N PRO A 153 " pdb=" C PRO A 153 " pdb=" CB PRO A 153 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1975 not shown) Planarity restraints: 2373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 798 " 0.198 2.00e-02 2.50e+03 2.81e-01 7.87e+02 pdb=" C PRO A 798 " -0.460 2.00e-02 2.50e+03 pdb=" O PRO A 798 " 0.254 2.00e-02 2.50e+03 pdb=" N ALA A 799 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 4 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO D 5 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 5 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 5 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 814 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO D 815 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 815 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 815 " 0.026 5.00e-02 4.00e+02 ... (remaining 2370 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 416 2.64 - 3.21: 13832 3.21 - 3.77: 20389 3.77 - 4.34: 27182 4.34 - 4.90: 41536 Nonbonded interactions: 103355 Sorted by model distance: nonbonded pdb=" O SER D 776 " pdb=" OG SER D 787 " model vdw 2.079 3.040 nonbonded pdb=" O LEU A 607 " pdb=" ND2 ASN A 609 " model vdw 2.121 3.120 nonbonded pdb=" OD1 ASN D 84 " pdb=" OG SER D 314 " model vdw 2.125 3.040 nonbonded pdb=" ND2 ASN D 339 " pdb=" OD1 ASN D 340 " model vdw 2.133 3.120 nonbonded pdb=" OG SER D 461 " pdb=" O GLY D 567 " model vdw 2.144 3.040 ... (remaining 103350 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 153 or resid 162 through 186 or (resid 187 and ( \ name N or name CA or name C or name O or name CB )) or resid 188 through 189 or \ resid 193 through 256 or resid 265 through 294 or resid 298 or resid 306 through \ 510 or resid 515 through 526 or resid 532 through 558 or resid 562 through 704 \ or resid 746 through 897)) selection = (chain 'D' and (resid 1 through 35 or resid 41 through 210 or resid 212 through \ 256 or resid 265 through 294 or resid 302 or resid 306 through 625 or resid 671 \ through 897)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.070 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.016 1.607 13525 Z= 1.049 Angle : 1.053 74.130 18360 Z= 0.676 Chirality : 0.050 0.179 1978 Planarity : 0.008 0.281 2373 Dihedral : 14.643 87.364 4995 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 18.16 % Favored : 81.65 % Rotamer: Outliers : 0.55 % Allowed : 11.95 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.21 (0.17), residues: 1602 helix: -4.27 (0.21), residues: 162 sheet: -3.01 (0.24), residues: 346 loop : -3.74 (0.16), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 240 TYR 0.026 0.002 TYR D 224 PHE 0.025 0.002 PHE D 793 TRP 0.021 0.002 TRP A 403 HIS 0.007 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.01573 / 1.05 (13493) covalent geometry : angle 1.05069 / 0.68 (18296) SS BOND : bond 0.00486 / 0.28 ( 32) SS BOND : angle 1.51294 / 1.06 ( 64) hydrogen bonds : bond 0.24984 / 16.73 ( 258) hydrogen bonds : angle 10.10773 / 6.99 ( 642) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3204 Ramachandran restraints generated. 1602 Oldfield, 0 Emsley, 1602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9109 (mmm) cc_final: 0.8387 (mmt) REVERT: A 222 ARG cc_start: 0.8572 (ttp-170) cc_final: 0.7980 (ttt180) REVERT: A 557 LEU cc_start: 0.8616 (mt) cc_final: 0.8280 (mt) REVERT: B 59 MET cc_start: 0.9015 (mtt) cc_final: 0.8311 (mtt) REVERT: D 100 LEU cc_start: 0.8614 (mt) cc_final: 0.8272 (mt) REVERT: D 176 TRP cc_start: 0.7309 (m100) cc_final: 0.6465 (m-10) REVERT: D 373 LEU cc_start: 0.9062 (mt) cc_final: 0.8848 (mp) REVERT: D 509 TYR cc_start: 0.6952 (m-80) cc_final: 0.6616 (m-80) REVERT: D 835 MET cc_start: 0.8655 (ptm) cc_final: 0.7491 (ptm) REVERT: D 851 VAL cc_start: 0.8411 (t) cc_final: 0.7654 (t) outliers start: 8 outliers final: 6 residues processed: 96 average time/residue: 0.1147 time to fit residues: 16.4600 Evaluate side-chains 65 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN A 14 GLN A 72 ASN A 169 ASN A 287 GLN A 334 ASN A 363 HIS A 397 GLN A 609 ASN A 830 ASN D 11 ASN D 102 ASN D 275 GLN D 578 ASN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 GLN ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.062109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049160 restraints weight = 76640.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049910 restraints weight = 45877.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050081 restraints weight = 36512.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050214 restraints weight = 33181.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050374 restraints weight = 30736.547| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13525 Z= 0.135 Angle : 0.680 15.917 18360 Z= 0.365 Chirality : 0.047 0.217 1978 Planarity : 0.005 0.050 2373 Dihedral : 6.443 49.201 1814 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.14 % Allowed : 5.49 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.00 (0.18), residues: 1604 helix: -2.93 (0.30), residues: 164 sheet: -2.39 (0.24), residues: 361 loop : -2.88 (0.17), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.021 0.001 TYR D 224 PHE 0.033 0.002 PHE A 893 TRP 0.014 0.001 TRP D 79 HIS 0.006 0.001 HIS D 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13493) covalent geometry : angle 0.67701 / 0.36 (18296) SS BOND : bond 0.00500 / 0.28 ( 32) SS BOND : angle 1.20111 / 0.83 ( 64) hydrogen bonds : bond 0.05144 / 3.47 ( 258) hydrogen bonds : angle 7.20430 / 5.01 ( 642) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.9068 (mmm) cc_final: 0.8718 (tpp) REVERT: A 119 LEU cc_start: 0.9522 (mm) cc_final: 0.9101 (mm) REVERT: A 268 ILE cc_start: 0.7482 (mp) cc_final: 0.6873 (mp) REVERT: A 522 MET cc_start: 0.8341 (ptm) cc_final: 0.8099 (ptm) REVERT: A 557 LEU cc_start: 0.8401 (mt) cc_final: 0.7993 (mm) REVERT: B 59 MET cc_start: 0.9205 (mtt) cc_final: 0.8824 (mtt) REVERT: D 100 LEU cc_start: 0.8796 (mt) cc_final: 0.8489 (mt) REVERT: D 176 TRP cc_start: 0.6907 (m100) cc_final: 0.6636 (m100) REVERT: D 313 ASP cc_start: 0.9090 (p0) cc_final: 0.8780 (p0) REVERT: D 835 MET cc_start: 0.8702 (ptm) cc_final: 0.8200 (ppp) REVERT: D 857 ARG cc_start: 0.9066 (mtp180) cc_final: 0.8863 (mtm-85) outliers start: 2 outliers final: 0 residues processed: 103 average time/residue: 0.1146 time to fit residues: 18.1295 Evaluate side-chains 60 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 162 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 15 optimal weight: 0.0170 chunk 48 optimal weight: 6.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 269 HIS B 15 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.062651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.049460 restraints weight = 74618.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050691 restraints weight = 45756.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050900 restraints weight = 33047.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051127 restraints weight = 28595.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.051358 restraints weight = 26463.434| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13525 Z= 0.116 Angle : 0.610 10.012 18360 Z= 0.325 Chirality : 0.046 0.172 1978 Planarity : 0.004 0.049 2373 Dihedral : 5.933 48.672 1814 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.20), residues: 1604 helix: -2.40 (0.33), residues: 166 sheet: -1.87 (0.26), residues: 359 loop : -2.44 (0.18), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 240 TYR 0.030 0.001 TYR D 224 PHE 0.024 0.001 PHE A 893 TRP 0.011 0.001 TRP A 405 HIS 0.003 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (13493) covalent geometry : angle 0.60664 / 0.32 (18296) SS BOND : bond 0.00356 / 0.23 ( 32) SS BOND : angle 1.22213 / 0.85 ( 64) hydrogen bonds : bond 0.04203 / 2.79 ( 258) hydrogen bonds : angle 6.45799 / 4.50 ( 642) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8187 (t0) cc_final: 0.7974 (t70) REVERT: A 118 ASP cc_start: 0.9216 (t0) cc_final: 0.8847 (t0) REVERT: A 119 LEU cc_start: 0.9462 (mm) cc_final: 0.9055 (mm) REVERT: A 268 ILE cc_start: 0.8183 (mp) cc_final: 0.7951 (mp) REVERT: A 522 MET cc_start: 0.8271 (ptm) cc_final: 0.7967 (ptm) REVERT: A 695 ASN cc_start: 0.9274 (m-40) cc_final: 0.8971 (m-40) REVERT: B 44 VAL cc_start: 0.9604 (m) cc_final: 0.9156 (p) REVERT: D 100 LEU cc_start: 0.8720 (mt) cc_final: 0.8416 (mt) REVERT: D 176 TRP cc_start: 0.6787 (m100) cc_final: 0.6575 (m100) REVERT: D 313 ASP cc_start: 0.9096 (p0) cc_final: 0.8808 (p0) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1118 time to fit residues: 16.2351 Evaluate side-chains 61 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 153 optimal weight: 50.0000 chunk 92 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 8.9990 chunk 162 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** A 564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 HIS D 365 HIS ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 ASN D 817 ASN D 877 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.059058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.045863 restraints weight = 77887.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.046597 restraints weight = 48831.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.046795 restraints weight = 38860.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.046958 restraints weight = 33666.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047142 restraints weight = 31367.859| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13525 Z= 0.346 Angle : 0.829 10.783 18360 Z= 0.426 Chirality : 0.050 0.203 1978 Planarity : 0.006 0.054 2373 Dihedral : 6.729 50.534 1814 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.65 % Favored : 86.35 % Rotamer: Outliers : 0.14 % Allowed : 5.43 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.19), residues: 1604 helix: -2.53 (0.33), residues: 165 sheet: -2.01 (0.26), residues: 370 loop : -2.55 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 240 TYR 0.024 0.002 TYR D 224 PHE 0.024 0.002 PHE A 391 TRP 0.021 0.002 TRP A 405 HIS 0.008 0.002 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.35 (13493) covalent geometry : angle 0.82236 / 0.42 (18296) SS BOND : bond 0.00590 / 0.35 ( 32) SS BOND : angle 2.00946 / 1.41 ( 64) hydrogen bonds : bond 0.04986 / 3.33 ( 258) hydrogen bonds : angle 6.96303 / 4.83 ( 642) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8552 (mp) cc_final: 0.8012 (mp) REVERT: A 522 MET cc_start: 0.8169 (ptm) cc_final: 0.7863 (ptm) REVERT: A 695 ASN cc_start: 0.9305 (m-40) cc_final: 0.9030 (t0) REVERT: D 100 LEU cc_start: 0.8754 (mt) cc_final: 0.8488 (mt) REVERT: D 176 TRP cc_start: 0.7243 (m100) cc_final: 0.6420 (m100) REVERT: D 313 ASP cc_start: 0.9085 (p0) cc_final: 0.8765 (p0) REVERT: D 835 MET cc_start: 0.8495 (ppp) cc_final: 0.7577 (ppp) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 0.0806 time to fit residues: 9.9890 Evaluate side-chains 52 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 84 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN A 388 ASN B 15 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.048085 restraints weight = 75947.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.048831 restraints weight = 48035.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.049126 restraints weight = 37434.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049292 restraints weight = 31791.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.049613 restraints weight = 29623.984| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13525 Z= 0.141 Angle : 0.641 10.133 18360 Z= 0.338 Chirality : 0.046 0.266 1978 Planarity : 0.004 0.048 2373 Dihedral : 6.149 48.845 1814 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.07 (0.20), residues: 1604 helix: -2.15 (0.35), residues: 161 sheet: -1.56 (0.27), residues: 357 loop : -2.32 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 489 TYR 0.028 0.001 TYR D 224 PHE 0.015 0.001 PHE A 893 TRP 0.010 0.001 TRP D 811 HIS 0.005 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13493) covalent geometry : angle 0.63020 / 0.33 (18296) SS BOND : bond 0.00396 / 0.22 ( 32) SS BOND : angle 2.12389 / 1.43 ( 64) hydrogen bonds : bond 0.04073 / 2.75 ( 258) hydrogen bonds : angle 6.42907 / 4.47 ( 642) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.8372 (mp) cc_final: 0.7691 (mm) REVERT: A 320 MET cc_start: 0.8633 (tmm) cc_final: 0.7969 (tmm) REVERT: A 321 LEU cc_start: 0.9360 (mt) cc_final: 0.9097 (mt) REVERT: A 522 MET cc_start: 0.8188 (ptm) cc_final: 0.7786 (ptm) REVERT: A 695 ASN cc_start: 0.9167 (m-40) cc_final: 0.8923 (t0) REVERT: D 100 LEU cc_start: 0.8796 (mt) cc_final: 0.8451 (mt) REVERT: D 176 TRP cc_start: 0.6955 (m100) cc_final: 0.6726 (m100) REVERT: D 313 ASP cc_start: 0.8993 (p0) cc_final: 0.8625 (p0) REVERT: D 373 LEU cc_start: 0.8882 (mt) cc_final: 0.8675 (mp) REVERT: D 835 MET cc_start: 0.8295 (ppp) cc_final: 0.7396 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0942 time to fit residues: 12.5478 Evaluate side-chains 55 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 87 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 52 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 695 ASN D 102 ASN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.048247 restraints weight = 74302.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.049494 restraints weight = 45467.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049717 restraints weight = 32489.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.049860 restraints weight = 28641.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.049999 restraints weight = 27143.999| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13525 Z= 0.128 Angle : 0.621 10.105 18360 Z= 0.326 Chirality : 0.046 0.220 1978 Planarity : 0.004 0.071 2373 Dihedral : 5.874 48.779 1814 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 0.14 % Allowed : 1.99 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.21), residues: 1604 helix: -1.79 (0.38), residues: 154 sheet: -1.35 (0.27), residues: 367 loop : -2.09 (0.19), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 240 TYR 0.025 0.001 TYR D 224 PHE 0.015 0.001 PHE A 893 TRP 0.011 0.001 TRP D 811 HIS 0.006 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (13493) covalent geometry : angle 0.61031 / 0.32 (18296) SS BOND : bond 0.00356 / 0.25 ( 32) SS BOND : angle 2.04114 / 1.40 ( 64) hydrogen bonds : bond 0.03845 / 2.57 ( 258) hydrogen bonds : angle 6.11793 / 4.27 ( 642) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 320 MET cc_start: 0.8552 (tmm) cc_final: 0.7890 (tmm) REVERT: A 321 LEU cc_start: 0.9339 (mt) cc_final: 0.9079 (mt) REVERT: A 522 MET cc_start: 0.8085 (ptm) cc_final: 0.7692 (ptm) REVERT: B 59 MET cc_start: 0.9238 (mtt) cc_final: 0.8825 (mtp) REVERT: D 100 LEU cc_start: 0.8755 (mt) cc_final: 0.8551 (mt) REVERT: D 176 TRP cc_start: 0.6875 (m100) cc_final: 0.6666 (m100) REVERT: D 313 ASP cc_start: 0.8934 (p0) cc_final: 0.8520 (p0) REVERT: D 373 LEU cc_start: 0.8881 (mt) cc_final: 0.8644 (mp) REVERT: D 835 MET cc_start: 0.8272 (ppp) cc_final: 0.7431 (ppp) REVERT: D 859 TYR cc_start: 0.8156 (m-10) cc_final: 0.7746 (m-10) outliers start: 2 outliers final: 0 residues processed: 83 average time/residue: 0.0919 time to fit residues: 12.4205 Evaluate side-chains 51 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 36 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 155 optimal weight: 0.3980 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 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 = 0.3287 r_free = 0.3287 target = 0.060190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.046612 restraints weight = 76655.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.047906 restraints weight = 48883.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.047979 restraints weight = 34785.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.048155 restraints weight = 31858.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.048240 restraints weight = 29124.618| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13525 Z= 0.261 Angle : 0.723 11.354 18360 Z= 0.375 Chirality : 0.048 0.210 1978 Planarity : 0.005 0.048 2373 Dihedral : 6.237 49.438 1814 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.66 % Favored : 87.34 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.20), residues: 1604 helix: -1.87 (0.37), residues: 156 sheet: -1.51 (0.27), residues: 374 loop : -2.17 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 377 TYR 0.020 0.002 TYR A 121 PHE 0.015 0.002 PHE A 749 TRP 0.015 0.002 TRP D 472 HIS 0.005 0.001 HIS D 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.26 (13493) covalent geometry : angle 0.71202 / 0.37 (18296) SS BOND : bond 0.00469 / 0.28 ( 32) SS BOND : angle 2.20799 / 1.48 ( 64) hydrogen bonds : bond 0.04237 / 2.83 ( 258) hydrogen bonds : angle 6.41747 / 4.49 ( 642) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 320 MET cc_start: 0.8654 (tmm) cc_final: 0.8089 (tmm) REVERT: A 522 MET cc_start: 0.8103 (ptm) cc_final: 0.7726 (ptm) REVERT: B 59 MET cc_start: 0.9201 (mtt) cc_final: 0.8775 (mtp) REVERT: D 176 TRP cc_start: 0.7088 (m100) cc_final: 0.6320 (m100) REVERT: D 313 ASP cc_start: 0.9011 (p0) cc_final: 0.8662 (p0) REVERT: D 835 MET cc_start: 0.8324 (ppp) cc_final: 0.7403 (ppp) REVERT: D 851 VAL cc_start: 0.8101 (t) cc_final: 0.7881 (t) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0866 time to fit residues: 9.7653 Evaluate side-chains 45 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 145 optimal weight: 0.0070 chunk 66 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 564 HIS B 15 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.047458 restraints weight = 75389.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048833 restraints weight = 47690.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.048959 restraints weight = 33522.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049185 restraints weight = 30058.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.049235 restraints weight = 27669.968| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13525 Z= 0.164 Angle : 0.638 10.003 18360 Z= 0.336 Chirality : 0.046 0.184 1978 Planarity : 0.004 0.048 2373 Dihedral : 5.970 48.859 1814 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 0.07 % Allowed : 0.89 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.21), residues: 1604 helix: -1.64 (0.38), residues: 155 sheet: -1.36 (0.27), residues: 373 loop : -2.05 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.025 0.001 TYR D 224 PHE 0.026 0.001 PHE D 503 TRP 0.016 0.001 TRP A 403 HIS 0.004 0.001 HIS A 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (13493) covalent geometry : angle 0.63031 / 0.33 (18296) SS BOND : bond 0.00374 / 0.23 ( 32) SS BOND : angle 1.82452 / 1.37 ( 64) hydrogen bonds : bond 0.03833 / 2.57 ( 258) hydrogen bonds : angle 6.18706 / 4.34 ( 642) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8500 (tmm) cc_final: 0.7941 (tpp) REVERT: A 320 MET cc_start: 0.8522 (tmm) cc_final: 0.8207 (tmm) REVERT: A 522 MET cc_start: 0.8015 (ptm) cc_final: 0.7622 (ptm) REVERT: B 59 MET cc_start: 0.9180 (mtt) cc_final: 0.8780 (mtp) REVERT: D 313 ASP cc_start: 0.8965 (p0) cc_final: 0.8595 (p0) REVERT: D 835 MET cc_start: 0.8326 (ppp) cc_final: 0.7410 (ppp) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.0872 time to fit residues: 10.6827 Evaluate side-chains 49 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 102 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 124 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.7964 > 50:) chunk 63 optimal weight: 0.6980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN D 102 ASN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.061669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047983 restraints weight = 75075.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.049331 restraints weight = 47419.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.049445 restraints weight = 32796.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.049587 restraints weight = 30203.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049771 restraints weight = 28281.060| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13525 Z= 0.134 Angle : 0.620 9.843 18360 Z= 0.324 Chirality : 0.045 0.180 1978 Planarity : 0.004 0.048 2373 Dihedral : 5.797 48.708 1814 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.21), residues: 1604 helix: -1.66 (0.38), residues: 161 sheet: -1.06 (0.29), residues: 352 loop : -1.98 (0.19), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.024 0.001 TYR D 224 PHE 0.016 0.001 PHE D 503 TRP 0.011 0.001 TRP A 405 HIS 0.003 0.001 HIS A 223 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (13493) covalent geometry : angle 0.61103 / 0.32 (18296) SS BOND : bond 0.00364 / 0.22 ( 32) SS BOND : angle 1.83845 / 1.29 ( 64) hydrogen bonds : bond 0.03707 / 2.45 ( 258) hydrogen bonds : angle 5.98760 / 4.22 ( 642) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8482 (tmm) cc_final: 0.7934 (tpp) REVERT: A 320 MET cc_start: 0.8512 (tmm) cc_final: 0.8235 (tmm) REVERT: A 321 LEU cc_start: 0.9254 (mp) cc_final: 0.9007 (mt) REVERT: A 522 MET cc_start: 0.8036 (ptm) cc_final: 0.7582 (ptm) REVERT: B 59 MET cc_start: 0.9237 (mtt) cc_final: 0.8863 (mtp) REVERT: D 313 ASP cc_start: 0.8914 (p0) cc_final: 0.8550 (p0) REVERT: D 835 MET cc_start: 0.8293 (ppp) cc_final: 0.7383 (ppp) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0941 time to fit residues: 11.3833 Evaluate side-chains 50 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 65 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 14 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS A 564 HIS B 15 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048968 restraints weight = 74620.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.049665 restraints weight = 44208.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.050081 restraints weight = 34082.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050197 restraints weight = 30246.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050339 restraints weight = 28027.512| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13525 Z= 0.112 Angle : 0.610 9.779 18360 Z= 0.318 Chirality : 0.046 0.188 1978 Planarity : 0.004 0.049 2373 Dihedral : 5.640 48.469 1814 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.07 % Allowed : 0.62 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.21), residues: 1604 helix: -1.71 (0.36), residues: 173 sheet: -1.06 (0.28), residues: 369 loop : -1.89 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 240 TYR 0.025 0.001 TYR D 224 PHE 0.015 0.001 PHE D 503 TRP 0.012 0.001 TRP A 405 HIS 0.003 0.001 HIS D 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (13493) covalent geometry : angle 0.60234 / 0.31 (18296) SS BOND : bond 0.00408 / 0.23 ( 32) SS BOND : angle 1.75711 / 1.16 ( 64) hydrogen bonds : bond 0.03514 / 2.34 ( 258) hydrogen bonds : angle 5.85322 / 4.13 ( 642) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3208 Ramachandran restraints generated. 1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 MET cc_start: 0.8500 (tmm) cc_final: 0.7930 (tpp) REVERT: A 320 MET cc_start: 0.8479 (tmm) cc_final: 0.8150 (tmm) REVERT: A 370 LEU cc_start: 0.8976 (mp) cc_final: 0.8274 (mt) REVERT: A 522 MET cc_start: 0.7991 (ptm) cc_final: 0.7475 (ptm) REVERT: D 313 ASP cc_start: 0.8833 (p0) cc_final: 0.8437 (p0) REVERT: D 835 MET cc_start: 0.8196 (ppp) cc_final: 0.7291 (ppp) REVERT: D 851 VAL cc_start: 0.7886 (t) cc_final: 0.7619 (t) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.0903 time to fit residues: 11.7715 Evaluate side-chains 60 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 26 optimal weight: 10.0000 chunk 112 optimal weight: 0.0980 chunk 75 optimal weight: 0.9980 chunk 93 optimal weight: 0.0570 chunk 157 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 97 optimal weight: 0.0770 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** D 609 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 632 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 = 0.3391 r_free = 0.3391 target = 0.063668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050075 restraints weight = 73663.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051438 restraints weight = 43475.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.051565 restraints weight = 30644.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.051725 restraints weight = 27728.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.051845 restraints weight = 26251.210| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13525 Z= 0.100 Angle : 0.593 9.554 18360 Z= 0.308 Chirality : 0.045 0.180 1978 Planarity : 0.004 0.049 2373 Dihedral : 5.384 48.036 1814 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.21), residues: 1604 helix: -1.61 (0.36), residues: 175 sheet: -0.90 (0.28), residues: 369 loop : -1.82 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 240 TYR 0.025 0.001 TYR D 224 PHE 0.013 0.001 PHE A 767 TRP 0.022 0.001 TRP A 403 HIS 0.003 0.001 HIS D 775 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (13493) covalent geometry : angle 0.58735 / 0.31 (18296) SS BOND : bond 0.00428 / 0.23 ( 32) SS BOND : angle 1.52386 / 1.00 ( 64) hydrogen bonds : bond 0.03320 / 2.20 ( 258) hydrogen bonds : angle 5.61663 / 3.99 ( 642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1834.91 seconds wall clock time: 32 minutes 46.09 seconds (1966.09 seconds total)