Starting phenix.real_space_refine on Thu Aug 6 08:41:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.map" model { file = "/net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u3k_63816/08_2026/9u3k_63816.cif" } resolution = 3.32 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 78 5.16 5 C 8946 2.51 5 N 2358 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14006 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 6957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6957 Classifications: {'peptide': 852} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 820} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1} Chain breaks: 1 Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Unusual residues: {'AMP%rna2p': 2} Classifications: {'RNA_mixed': 2} Modifications used: {'rna2p': 2} Link IDs: {'rna2p': 1} Chain breaks: 1 Time building chain proxies: 3.33, per 1000 atoms: 0.24 Number of scatterers: 14006 At special positions: 0 Unit cell: (169.32, 126.16, 128.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 78 16.00 P 6 15.00 O 2618 8.00 N 2358 7.00 C 8946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.22 Conformation dependent library (CDL) restraints added in 494.2 milliseconds 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 15 sheets defined 49.8% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 35 through 40 removed outlier: 3.914A pdb=" N TRP D 38 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TRP D 40 " --> pdb=" O TRP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.702A pdb=" N ARG D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 59 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 71 through 81 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.963A pdb=" N ILE D 237 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR D 238 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 267 Processing helix chain 'D' and resid 283 through 297 removed outlier: 3.557A pdb=" N ASP D 296 " --> pdb=" O TYR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 309 Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.749A pdb=" N LYS D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 366 through 373 Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'D' and resid 400 through 404 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 420 through 431 Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.535A pdb=" N TRP D 445 " --> pdb=" O ASN D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 451 Processing helix chain 'D' and resid 452 through 482 Processing helix chain 'D' and resid 485 through 487 No H-bonds generated for 'chain 'D' and resid 485 through 487' Processing helix chain 'D' and resid 488 through 494 Processing helix chain 'D' and resid 510 through 520 removed outlier: 6.496A pdb=" N ALA D 515 " --> pdb=" O TYR D 512 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N HIS D 516 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 517 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 518 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 530 removed outlier: 3.701A pdb=" N LEU D 525 " --> pdb=" O ASP D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 563 removed outlier: 3.550A pdb=" N GLN D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 589 removed outlier: 3.616A pdb=" N VAL D 589 " --> pdb=" O LEU D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 613 removed outlier: 4.010A pdb=" N MET D 612 " --> pdb=" O GLU D 608 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN D 613 " --> pdb=" O LLP D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 629 Processing helix chain 'D' and resid 645 through 664 Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 678 through 692 Processing helix chain 'D' and resid 693 through 696 Processing helix chain 'D' and resid 697 through 709 Processing helix chain 'D' and resid 709 through 741 removed outlier: 3.559A pdb=" N ALA D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN D 723 " --> pdb=" O LYS D 719 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP D 724 " --> pdb=" O LEU D 720 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN D 725 " --> pdb=" O SER D 721 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU D 727 " --> pdb=" O ASN D 723 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA D 728 " --> pdb=" O ASP D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 757 removed outlier: 4.163A pdb=" N ALA D 757 " --> pdb=" O CYS D 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 34 removed outlier: 4.262A pdb=" N GLU E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 40 removed outlier: 3.665A pdb=" N TRP E 40 " --> pdb=" O TRP E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 37 through 40' Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.772A pdb=" N ASP E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 59 Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 73 through 81 removed outlier: 4.496A pdb=" N VAL E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 Processing helix chain 'E' and resid 128 through 144 Processing helix chain 'E' and resid 234 through 239 removed outlier: 3.758A pdb=" N THR E 238 " --> pdb=" O ARG E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 268 removed outlier: 3.964A pdb=" N LEU E 250 " --> pdb=" O TRP E 246 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 282 Processing helix chain 'E' and resid 283 through 296 Processing helix chain 'E' and resid 299 through 310 Processing helix chain 'E' and resid 319 through 323 Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.679A pdb=" N TYR E 334 " --> pdb=" O LEU E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.825A pdb=" N ARG E 341 " --> pdb=" O GLY E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 352 Processing helix chain 'E' and resid 366 through 374 Processing helix chain 'E' and resid 381 through 392 Processing helix chain 'E' and resid 393 through 396 Processing helix chain 'E' and resid 400 through 404 Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 420 through 431 Processing helix chain 'E' and resid 435 through 439 removed outlier: 4.287A pdb=" N GLN E 439 " --> pdb=" O MET E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 4.012A pdb=" N TRP E 445 " --> pdb=" O ASN E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 452 through 482 removed outlier: 3.707A pdb=" N ASN E 482 " --> pdb=" O THR E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 485 through 487 No H-bonds generated for 'chain 'E' and resid 485 through 487' Processing helix chain 'E' and resid 488 through 494 Processing helix chain 'E' and resid 510 through 514 Processing helix chain 'E' and resid 521 through 530 Processing helix chain 'E' and resid 548 through 563 removed outlier: 3.920A pdb=" N GLN E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 589 removed outlier: 3.976A pdb=" N SER E 587 " --> pdb=" O ARG E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 613 removed outlier: 3.700A pdb=" N MET E 612 " --> pdb=" O GLU E 608 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN E 613 " --> pdb=" O LLP E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 629 Processing helix chain 'E' and resid 645 through 662 Processing helix chain 'E' and resid 664 through 670 Processing helix chain 'E' and resid 678 through 692 Processing helix chain 'E' and resid 693 through 696 Processing helix chain 'E' and resid 697 through 709 removed outlier: 3.525A pdb=" N GLN E 701 " --> pdb=" O THR E 697 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 720 Processing helix chain 'E' and resid 727 through 741 Processing helix chain 'E' and resid 742 through 745 removed outlier: 3.614A pdb=" N ILE E 745 " --> pdb=" O TRP E 742 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 742 through 745' Processing sheet with id=AA1, first strand: chain 'E' and resid 757 through 759 removed outlier: 4.236A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N SER E 825 " --> pdb=" O GLU E 788 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU E 788 " --> pdb=" O SER E 825 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LYS E 787 " --> pdb=" O VAL E 796 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL E 796 " --> pdb=" O LYS E 787 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN E 789 " --> pdb=" O LYS E 794 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N LYS E 794 " --> pdb=" O GLN E 789 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 757 through 759 removed outlier: 4.236A pdb=" N ALA E 758 " --> pdb=" O THR D 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AA4, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.530A pdb=" N LEU D 222 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N MET D 148 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N TYR D 221 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA D 150 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 223 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY D 152 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA D 111 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ASN D 277 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE D 113 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 376 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL D 377 " --> pdb=" O GLY D 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 162 through 164 Processing sheet with id=AA6, first strand: chain 'D' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'D' and resid 571 through 573 removed outlier: 3.554A pdb=" N SER D 541 " --> pdb=" O PHE D 505 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET D 502 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET D 593 " --> pdb=" O MET D 502 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY D 504 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN D 617 " --> pdb=" O TRP D 635 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU D 637 " --> pdb=" O ASN D 617 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER D 619 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 746 through 751 removed outlier: 6.285A pdb=" N VAL D 747 " --> pdb=" O ASP D 771 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP D 771 " --> pdb=" O VAL D 747 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 749 " --> pdb=" O VAL D 769 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 818 " --> pdb=" O ILE D 764 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 766 " --> pdb=" O ALA D 816 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY D 806 " --> pdb=" O THR D 813 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLU D 815 " --> pdb=" O MET D 804 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET D 804 " --> pdb=" O GLU D 815 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 794 through 801 removed outlier: 6.781A pdb=" N LYS D 794 " --> pdb=" O GLN D 789 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLN D 789 " --> pdb=" O LYS D 794 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL D 796 " --> pdb=" O LYS D 787 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N LYS D 787 " --> pdb=" O VAL D 796 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 827 " --> pdb=" O LEU D 786 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL D 830 " --> pdb=" O LEU D 851 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 185 through 186 Processing sheet with id=AB2, first strand: chain 'E' and resid 185 through 186 removed outlier: 7.191A pdb=" N MET E 148 " --> pdb=" O LYS E 219 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N TYR E 221 " --> pdb=" O MET E 148 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA E 150 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU E 223 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY E 152 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL E 110 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL E 151 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR E 112 " --> pdb=" O VAL E 151 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N PHE E 153 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR E 274 " --> pdb=" O LEU E 312 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR E 314 " --> pdb=" O TYR E 274 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS E 276 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER E 311 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ASN E 378 " --> pdb=" O SER E 311 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR E 313 " --> pdb=" O ASN E 378 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 377 " --> pdb=" O GLY E 407 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AB5, first strand: chain 'E' and resid 571 through 574 removed outlier: 5.197A pdb=" N CYS E 506 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TRP E 592 " --> pdb=" O LEU E 618 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL E 620 " --> pdb=" O TRP E 592 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN E 594 " --> pdb=" O VAL E 620 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASN E 617 " --> pdb=" O TRP E 635 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N LEU E 637 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N SER E 619 " --> pdb=" O LEU E 637 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 746 through 747 removed outlier: 3.641A pdb=" N HIS E 746 " --> pdb=" O ASP E 771 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASN E 811 " --> pdb=" O HIS E 807 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N HIS E 807 " --> pdb=" O ASN E 811 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR E 813 " --> pdb=" O VAL E 805 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1764 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: 2.97 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2349 1.31 - 1.43: 4041 1.43 - 1.56: 7846 1.56 - 1.68: 6 1.68 - 1.81: 130 Bond restraints: 14372 Sorted by residual: bond pdb=" OP4 LLP D 609 " pdb=" P LLP D 609 " ideal model delta sigma weight residual 1.726 1.606 0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" OP4 LLP E 609 " pdb=" P LLP E 609 " ideal model delta sigma weight residual 1.726 1.611 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C4 AMP D 901 " pdb=" C5 AMP D 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C4 AMP E 902 " pdb=" C5 AMP E 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C4 AMP D 902 " pdb=" C5 AMP D 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 ... (remaining 14367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 19011 2.65 - 5.30: 380 5.30 - 7.95: 68 7.95 - 10.60: 14 10.60 - 13.25: 1 Bond angle restraints: 19474 Sorted by residual: angle pdb=" N ARG D 583 " pdb=" CA ARG D 583 " pdb=" C ARG D 583 " ideal model delta sigma weight residual 113.72 100.47 13.25 1.30e+00 5.92e-01 1.04e+02 angle pdb=" C PRO E 200 " pdb=" CA PRO E 200 " pdb=" CB PRO E 200 " ideal model delta sigma weight residual 111.56 101.71 9.85 1.09e+00 8.42e-01 8.17e+01 angle pdb=" N ASN E 248 " pdb=" CA ASN E 248 " pdb=" C ASN E 248 " ideal model delta sigma weight residual 111.14 103.30 7.84 1.08e+00 8.57e-01 5.27e+01 angle pdb=" N GLN E 252 " pdb=" CA GLN E 252 " pdb=" C GLN E 252 " ideal model delta sigma weight residual 113.41 104.71 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" N ALA E 728 " pdb=" CA ALA E 728 " pdb=" C ALA E 728 " ideal model delta sigma weight residual 111.07 103.45 7.62 1.07e+00 8.73e-01 5.07e+01 ... (remaining 19469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 8102 35.66 - 71.32: 347 71.32 - 106.99: 24 106.99 - 142.65: 2 142.65 - 178.31: 3 Dihedral angle restraints: 8478 sinusoidal: 3496 harmonic: 4982 Sorted by residual: dihedral pdb=" C2' AMP E 902 " pdb=" C1' AMP E 902 " pdb=" N9 AMP E 902 " pdb=" C4 AMP E 902 " ideal model delta sinusoidal sigma weight residual 91.55 -90.14 -178.31 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2' AMP E 901 " pdb=" C1' AMP E 901 " pdb=" N9 AMP E 901 " pdb=" C4 AMP E 901 " ideal model delta sinusoidal sigma weight residual 91.55 -85.87 177.42 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2' AMP D 902 " pdb=" C1' AMP D 902 " pdb=" N9 AMP D 902 " pdb=" C4 AMP D 902 " ideal model delta sinusoidal sigma weight residual 91.55 -62.88 154.43 1 2.00e+01 2.50e-03 4.56e+01 ... (remaining 8475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1455 0.054 - 0.109: 449 0.109 - 0.163: 88 0.163 - 0.217: 13 0.217 - 0.272: 7 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA VAL D 319 " pdb=" N VAL D 319 " pdb=" C VAL D 319 " pdb=" CB VAL D 319 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL D 315 " pdb=" CA VAL D 315 " pdb=" CG1 VAL D 315 " pdb=" CG2 VAL D 315 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ARG D 583 " pdb=" N ARG D 583 " pdb=" C ARG D 583 " pdb=" CB ARG D 583 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2009 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP E 609 " -0.082 2.00e-02 2.50e+03 8.52e-02 7.26e+01 pdb=" NZ LLP E 609 " 0.072 2.00e-02 2.50e+03 pdb=" C4 LLP E 609 " -0.087 2.00e-02 2.50e+03 pdb=" C4' LLP E 609 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 515 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ALA E 515 " -0.066 2.00e-02 2.50e+03 pdb=" O ALA E 515 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS E 516 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 245 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C ASP E 245 " 0.046 2.00e-02 2.50e+03 pdb=" O ASP E 245 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP E 246 " -0.015 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2460 2.75 - 3.29: 12998 3.29 - 3.82: 23310 3.82 - 4.36: 27830 4.36 - 4.90: 49317 Nonbonded interactions: 115915 Sorted by model distance: nonbonded pdb=" OE1 GLN E 121 " pdb=" OG1 THR E 580 " model vdw 2.212 3.040 nonbonded pdb=" OE2 GLU D 140 " pdb=" OG SER D 144 " model vdw 2.215 3.040 nonbonded pdb=" OE2 GLU E 116 " pdb=" OH TYR E 242 " model vdw 2.227 3.040 nonbonded pdb=" OE2 GLU D 116 " pdb=" OH TYR D 242 " model vdw 2.233 3.040 nonbonded pdb=" O LEU D 518 " pdb=" OH TYR D 658 " model vdw 2.237 3.040 ... (remaining 115910 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: 0.03 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.370 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.670 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 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 : 0.011 0.120 14372 Z= 0.497 Angle : 0.949 13.254 19474 Z= 0.557 Chirality : 0.055 0.272 2012 Planarity : 0.005 0.085 2502 Dihedral : 18.834 178.310 5298 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.61 % Favored : 94.04 % Rotamer: Outliers : 4.48 % Allowed : 21.57 % Favored : 73.95 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1694 helix: -0.01 (0.19), residues: 688 sheet: -0.35 (0.33), residues: 259 loop : -1.64 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 741 TYR 0.030 0.002 TYR E 204 PHE 0.020 0.002 PHE E 160 TRP 0.027 0.002 TRP D 40 HIS 0.010 0.002 HIS D 316 Details of bonding type rmsd/Z covalent geometry : bond 0.01058 / 0.50 (14372) covalent geometry : angle 0.94884 / 0.56 (19474) hydrogen bonds : bond 0.17445 / 11.46 ( 625) hydrogen bonds : angle 7.40003 / 5.20 ( 1764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 126 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 185 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8202 (tt0) REVERT: D 201 TYR cc_start: 0.8515 (m-80) cc_final: 0.7620 (m-80) REVERT: D 305 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: D 306 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9053 (mp) REVERT: D 356 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7547 (p0) REVERT: D 430 TYR cc_start: 0.8679 (m-80) cc_final: 0.8162 (m-80) REVERT: D 583 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8440 (mtp180) REVERT: D 662 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8093 (mm-30) REVERT: D 674 LYS cc_start: 0.8564 (tppt) cc_final: 0.8266 (mtmt) REVERT: D 750 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8343 (tttt) REVERT: D 754 MET cc_start: 0.6773 (ttt) cc_final: 0.6375 (ttt) REVERT: D 787 LYS cc_start: 0.5487 (mttt) cc_final: 0.5106 (mmtt) REVERT: D 835 LYS cc_start: 0.8697 (tttp) cc_final: 0.8426 (ttmt) REVERT: D 844 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7290 (m-30) REVERT: E 67 LEU cc_start: 0.8331 (mt) cc_final: 0.7977 (mm) REVERT: E 106 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8581 (ttmm) REVERT: E 191 ASN cc_start: 0.8031 (m-40) cc_final: 0.7268 (t0) REVERT: E 204 TYR cc_start: 0.8263 (OUTLIER) cc_final: 0.7905 (p90) REVERT: E 359 ASP cc_start: 0.8086 (t0) cc_final: 0.7807 (t70) REVERT: E 651 GLN cc_start: 0.8885 (tp-100) cc_final: 0.8648 (tt0) REVERT: E 683 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8509 (mm-40) REVERT: E 720 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8891 (tp) REVERT: E 763 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8715 (tmtt) outliers start: 66 outliers final: 45 residues processed: 181 average time/residue: 0.1132 time to fit residues: 30.5116 Evaluate side-chains 173 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 170 GLN Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 356 ASN Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 395 ILE Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 583 ARG Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 844 ASP Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 106 LYS Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 204 TYR Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 246 TRP Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 468 VAL Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain E residue 683 GLN Chi-restraints excluded: chain E residue 720 LEU Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 750 LYS Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 760 THR Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 822 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 316 HIS D 446 HIS E 205 GLN E 301 ASN E 499 ASN E 552 GLN E 723 ASN E 725 ASN E 843 GLN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104115 restraints weight = 23862.304| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.29 r_work: 0.3216 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14372 Z= 0.124 Angle : 0.559 7.806 19474 Z= 0.280 Chirality : 0.042 0.133 2012 Planarity : 0.004 0.051 2502 Dihedral : 11.662 179.283 2033 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Rotamer: Outliers : 3.46 % Allowed : 19.67 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1694 helix: 0.71 (0.19), residues: 693 sheet: 0.03 (0.32), residues: 262 loop : -1.30 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 741 TYR 0.017 0.001 TYR D 696 PHE 0.015 0.001 PHE E 160 TRP 0.012 0.001 TRP D 418 HIS 0.007 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (14372) covalent geometry : angle 0.55856 / 0.28 (19474) hydrogen bonds : bond 0.04099 / 2.58 ( 625) hydrogen bonds : angle 5.05345 / 3.55 ( 1764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8861 (tt) REVERT: D 201 TYR cc_start: 0.8219 (m-80) cc_final: 0.7420 (m-80) REVERT: D 305 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: D 390 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: D 430 TYR cc_start: 0.8844 (m-80) cc_final: 0.8400 (m-80) REVERT: D 612 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8279 (mmt) REVERT: D 644 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6594 (pm20) REVERT: D 662 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7618 (mm-30) REVERT: D 750 LYS cc_start: 0.8520 (ttpt) cc_final: 0.8235 (tttt) REVERT: D 754 MET cc_start: 0.7114 (ttt) cc_final: 0.6825 (ttt) REVERT: D 787 LYS cc_start: 0.5494 (mttt) cc_final: 0.5160 (mmmt) REVERT: D 817 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7026 (tm-30) REVERT: D 835 LYS cc_start: 0.8653 (tttp) cc_final: 0.8320 (ttmt) REVERT: E 85 MET cc_start: 0.8072 (tpp) cc_final: 0.7683 (tpp) REVERT: E 106 LYS cc_start: 0.8901 (mtmm) cc_final: 0.8548 (ttmm) REVERT: E 191 ASN cc_start: 0.8050 (m-40) cc_final: 0.7391 (t0) REVERT: E 335 MET cc_start: 0.9013 (mmt) cc_final: 0.8719 (mmt) REVERT: E 359 ASP cc_start: 0.7908 (t0) cc_final: 0.7532 (t70) REVERT: E 683 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7851 (mm110) REVERT: E 754 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7544 (pmm) REVERT: E 763 LYS cc_start: 0.8858 (tmmm) cc_final: 0.8475 (tmtt) outliers start: 51 outliers final: 27 residues processed: 177 average time/residue: 0.1071 time to fit residues: 28.2492 Evaluate side-chains 150 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 511 THR Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 683 GLN Chi-restraints excluded: chain E residue 743 ASP Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 87 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 74 optimal weight: 8.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 446 HIS D 545 HIS E 169 GLN E 205 GLN E 683 GLN ** E 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102280 restraints weight = 24038.242| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.29 r_work: 0.3141 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14372 Z= 0.167 Angle : 0.552 6.066 19474 Z= 0.276 Chirality : 0.042 0.132 2012 Planarity : 0.004 0.051 2502 Dihedral : 10.609 178.674 1966 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 2.99 % Allowed : 19.67 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.20), residues: 1694 helix: 0.92 (0.20), residues: 694 sheet: 0.22 (0.32), residues: 259 loop : -1.19 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 74 TYR 0.017 0.001 TYR D 696 PHE 0.015 0.001 PHE E 160 TRP 0.013 0.001 TRP D 40 HIS 0.005 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (14372) covalent geometry : angle 0.55156 / 0.28 (19474) hydrogen bonds : bond 0.04065 / 2.55 ( 625) hydrogen bonds : angle 4.82821 / 3.40 ( 1764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8848 (tt) REVERT: D 201 TYR cc_start: 0.8325 (m-80) cc_final: 0.7372 (m-80) REVERT: D 250 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9185 (tp) REVERT: D 305 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: D 306 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8948 (mp) REVERT: D 347 ASP cc_start: 0.8319 (t70) cc_final: 0.7598 (p0) REVERT: D 390 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: D 430 TYR cc_start: 0.8891 (m-80) cc_final: 0.8438 (m-80) REVERT: D 533 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8662 (mt-10) REVERT: D 612 MET cc_start: 0.9091 (mmt) cc_final: 0.8762 (mmt) REVERT: D 662 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7628 (mm-30) REVERT: D 750 LYS cc_start: 0.8563 (ttpt) cc_final: 0.8297 (tttt) REVERT: D 754 MET cc_start: 0.7114 (ttt) cc_final: 0.6771 (ttt) REVERT: D 817 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 835 LYS cc_start: 0.8694 (tttp) cc_final: 0.8311 (ttmt) REVERT: E 74 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8519 (mmm160) REVERT: E 106 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8519 (ttmm) REVERT: E 191 ASN cc_start: 0.8094 (m-40) cc_final: 0.7399 (t0) REVERT: E 359 ASP cc_start: 0.7898 (t0) cc_final: 0.7536 (t70) REVERT: E 683 GLN cc_start: 0.8494 (tp40) cc_final: 0.7909 (mm110) REVERT: E 763 LYS cc_start: 0.8864 (tmmm) cc_final: 0.8520 (tmtt) outliers start: 44 outliers final: 31 residues processed: 160 average time/residue: 0.1200 time to fit residues: 28.6452 Evaluate side-chains 152 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 166 MET Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 178 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.101418 restraints weight = 24276.441| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.28 r_work: 0.3123 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8952 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14372 Z= 0.211 Angle : 0.573 6.086 19474 Z= 0.287 Chirality : 0.043 0.132 2012 Planarity : 0.004 0.051 2502 Dihedral : 10.252 178.460 1956 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 3.87 % Allowed : 19.34 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.20), residues: 1694 helix: 0.87 (0.20), residues: 703 sheet: 0.21 (0.32), residues: 262 loop : -1.13 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 741 TYR 0.018 0.001 TYR D 696 PHE 0.016 0.001 PHE E 160 TRP 0.015 0.001 TRP D 40 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (14372) covalent geometry : angle 0.57255 / 0.29 (19474) hydrogen bonds : bond 0.04170 / 2.62 ( 625) hydrogen bonds : angle 4.80779 / 3.40 ( 1764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8906 (tt) REVERT: D 201 TYR cc_start: 0.8304 (m-80) cc_final: 0.7312 (m-80) REVERT: D 305 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: D 306 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 347 ASP cc_start: 0.8297 (t70) cc_final: 0.7618 (p0) REVERT: D 390 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: D 430 TYR cc_start: 0.8862 (m-80) cc_final: 0.8376 (m-80) REVERT: D 612 MET cc_start: 0.9082 (mmt) cc_final: 0.8852 (mmt) REVERT: D 662 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7757 (mm-30) REVERT: D 817 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 835 LYS cc_start: 0.8727 (tttp) cc_final: 0.8342 (ttpt) REVERT: E 106 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8558 (ttmm) REVERT: E 191 ASN cc_start: 0.8150 (m-40) cc_final: 0.7411 (t0) REVERT: E 205 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: E 683 GLN cc_start: 0.8546 (tp40) cc_final: 0.7951 (mm110) REVERT: E 763 LYS cc_start: 0.8859 (tmmm) cc_final: 0.8447 (tmtt) outliers start: 57 outliers final: 36 residues processed: 165 average time/residue: 0.1117 time to fit residues: 28.0614 Evaluate side-chains 149 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 239 TYR Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 807 HIS Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 605 THR Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 831 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 13 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.0770 chunk 133 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 56 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 617 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104684 restraints weight = 23956.342| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.24 r_work: 0.3233 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14372 Z= 0.103 Angle : 0.506 5.981 19474 Z= 0.250 Chirality : 0.040 0.128 2012 Planarity : 0.003 0.052 2502 Dihedral : 9.828 179.680 1956 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.84 % Favored : 96.10 % Rotamer: Outliers : 2.58 % Allowed : 20.96 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1694 helix: 1.07 (0.20), residues: 709 sheet: 0.51 (0.33), residues: 267 loop : -0.99 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 741 TYR 0.014 0.001 TYR D 696 PHE 0.015 0.001 PHE E 160 TRP 0.009 0.001 TRP D 346 HIS 0.006 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (14372) covalent geometry : angle 0.50618 / 0.25 (19474) hydrogen bonds : bond 0.03470 / 2.18 ( 625) hydrogen bonds : angle 4.45896 / 3.15 ( 1764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8890 (tt) REVERT: D 159 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8520 (t80) REVERT: D 305 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: D 306 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8915 (mp) REVERT: D 347 ASP cc_start: 0.8197 (t70) cc_final: 0.7532 (p0) REVERT: D 390 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: D 430 TYR cc_start: 0.8886 (m-80) cc_final: 0.8521 (m-80) REVERT: D 612 MET cc_start: 0.9048 (mmt) cc_final: 0.8750 (mmt) REVERT: D 662 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7584 (mm-30) REVERT: D 817 GLU cc_start: 0.7519 (tm-30) cc_final: 0.7110 (tm-30) REVERT: D 835 LYS cc_start: 0.8691 (tttp) cc_final: 0.8322 (ttpt) REVERT: E 106 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8639 (ttmm) REVERT: E 191 ASN cc_start: 0.8088 (m-40) cc_final: 0.7349 (t0) REVERT: E 295 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7772 (mt-10) REVERT: E 683 GLN cc_start: 0.8417 (tp40) cc_final: 0.7859 (mm110) REVERT: E 763 LYS cc_start: 0.8802 (tmmm) cc_final: 0.8474 (tmtt) outliers start: 38 outliers final: 26 residues processed: 164 average time/residue: 0.1136 time to fit residues: 27.8776 Evaluate side-chains 144 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 29 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.125107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.103097 restraints weight = 23905.968| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.28 r_work: 0.3199 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14372 Z= 0.176 Angle : 0.549 8.194 19474 Z= 0.273 Chirality : 0.042 0.136 2012 Planarity : 0.004 0.051 2502 Dihedral : 9.669 179.034 1951 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.37 % Favored : 95.57 % Rotamer: Outliers : 2.44 % Allowed : 21.37 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.20), residues: 1694 helix: 1.06 (0.20), residues: 707 sheet: 0.60 (0.33), residues: 265 loop : -1.02 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 741 TYR 0.024 0.001 TYR D 696 PHE 0.016 0.001 PHE E 160 TRP 0.013 0.001 TRP D 40 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (14372) covalent geometry : angle 0.54913 / 0.27 (19474) hydrogen bonds : bond 0.03852 / 2.42 ( 625) hydrogen bonds : angle 4.56287 / 3.23 ( 1764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8942 (tt) REVERT: D 306 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8937 (mp) REVERT: D 347 ASP cc_start: 0.8246 (t70) cc_final: 0.7591 (p0) REVERT: D 390 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: D 430 TYR cc_start: 0.8871 (m-80) cc_final: 0.8423 (m-80) REVERT: D 662 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7743 (mm-30) REVERT: D 817 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7109 (tm-30) REVERT: D 835 LYS cc_start: 0.8714 (tttp) cc_final: 0.8337 (ttpt) REVERT: E 106 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8648 (ttmm) REVERT: E 191 ASN cc_start: 0.8140 (m-40) cc_final: 0.7346 (t0) REVERT: E 295 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7804 (mt-10) REVERT: E 683 GLN cc_start: 0.8514 (tp40) cc_final: 0.7966 (mm110) REVERT: E 763 LYS cc_start: 0.8819 (tmmm) cc_final: 0.8442 (tmtt) outliers start: 36 outliers final: 27 residues processed: 147 average time/residue: 0.1001 time to fit residues: 22.5367 Evaluate side-chains 141 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 122 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.102557 restraints weight = 23954.373| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.30 r_work: 0.3144 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14372 Z= 0.177 Angle : 0.549 8.291 19474 Z= 0.273 Chirality : 0.042 0.132 2012 Planarity : 0.004 0.049 2502 Dihedral : 9.549 179.140 1945 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 2.71 % Allowed : 21.10 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1694 helix: 0.96 (0.20), residues: 717 sheet: 0.65 (0.33), residues: 260 loop : -1.01 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 424 TYR 0.023 0.001 TYR D 696 PHE 0.015 0.001 PHE E 160 TRP 0.012 0.001 TRP D 40 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (14372) covalent geometry : angle 0.54915 / 0.27 (19474) hydrogen bonds : bond 0.03867 / 2.43 ( 625) hydrogen bonds : angle 4.57077 / 3.24 ( 1764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8941 (tt) REVERT: D 306 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8918 (mp) REVERT: D 347 ASP cc_start: 0.8178 (t70) cc_final: 0.7523 (p0) REVERT: D 390 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: D 430 TYR cc_start: 0.8841 (m-80) cc_final: 0.8376 (m-80) REVERT: D 662 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7707 (mm-30) REVERT: D 835 LYS cc_start: 0.8730 (tttp) cc_final: 0.8309 (ttpt) REVERT: E 106 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8663 (ttmm) REVERT: E 191 ASN cc_start: 0.8202 (m-40) cc_final: 0.7387 (t0) REVERT: E 205 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: E 295 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7871 (mt-10) REVERT: E 683 GLN cc_start: 0.8529 (tp40) cc_final: 0.7975 (mm110) REVERT: E 763 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8407 (tmtt) REVERT: E 827 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8390 (mtmt) outliers start: 40 outliers final: 33 residues processed: 149 average time/residue: 0.1147 time to fit residues: 25.7329 Evaluate side-chains 148 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 746 HIS Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.2980 chunk 154 optimal weight: 0.5980 chunk 140 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 789 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103207 restraints weight = 23772.380| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.29 r_work: 0.3208 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14372 Z= 0.154 Angle : 0.542 8.160 19474 Z= 0.269 Chirality : 0.041 0.132 2012 Planarity : 0.004 0.050 2502 Dihedral : 9.465 179.517 1945 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.92 % Allowed : 21.44 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.20), residues: 1694 helix: 1.04 (0.20), residues: 714 sheet: 0.69 (0.33), residues: 260 loop : -0.98 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 424 TYR 0.017 0.001 TYR D 696 PHE 0.015 0.001 PHE E 160 TRP 0.012 0.001 TRP D 850 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (14372) covalent geometry : angle 0.54154 / 0.27 (19474) hydrogen bonds : bond 0.03739 / 2.35 ( 625) hydrogen bonds : angle 4.50267 / 3.19 ( 1764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8948 (tt) REVERT: D 159 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8703 (t80) REVERT: D 306 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8924 (mp) REVERT: D 347 ASP cc_start: 0.8165 (t70) cc_final: 0.7538 (p0) REVERT: D 390 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: D 430 TYR cc_start: 0.8830 (m-80) cc_final: 0.8387 (m-80) REVERT: D 578 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8039 (t0) REVERT: D 662 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7708 (mm-30) REVERT: D 835 LYS cc_start: 0.8729 (tttp) cc_final: 0.8327 (ttpt) REVERT: E 106 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8643 (ttmm) REVERT: E 166 MET cc_start: 0.6656 (mtp) cc_final: 0.6158 (mtt) REVERT: E 191 ASN cc_start: 0.8190 (m-40) cc_final: 0.7362 (t0) REVERT: E 205 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: E 250 LEU cc_start: 0.9201 (tp) cc_final: 0.8836 (tt) REVERT: E 295 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7851 (mt-10) REVERT: E 683 GLN cc_start: 0.8495 (tp40) cc_final: 0.7960 (mm110) REVERT: E 763 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8387 (tmtt) outliers start: 43 outliers final: 30 residues processed: 149 average time/residue: 0.1117 time to fit residues: 25.6159 Evaluate side-chains 146 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 789 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.101153 restraints weight = 24242.387| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.28 r_work: 0.3107 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 14372 Z= 0.263 Angle : 0.615 9.078 19474 Z= 0.308 Chirality : 0.044 0.133 2012 Planarity : 0.004 0.048 2502 Dihedral : 9.625 178.653 1945 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.86 % Rotamer: Outliers : 2.99 % Allowed : 21.37 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1694 helix: 0.94 (0.19), residues: 703 sheet: 0.60 (0.33), residues: 256 loop : -1.10 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 424 TYR 0.023 0.001 TYR D 696 PHE 0.016 0.002 PHE E 160 TRP 0.016 0.001 TRP D 40 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (14372) covalent geometry : angle 0.61466 / 0.31 (19474) hydrogen bonds : bond 0.04279 / 2.70 ( 625) hydrogen bonds : angle 4.74783 / 3.37 ( 1764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 106 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8941 (tt) REVERT: D 159 TYR cc_start: 0.9154 (OUTLIER) cc_final: 0.8735 (t80) REVERT: D 306 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8929 (mp) REVERT: D 347 ASP cc_start: 0.8206 (t70) cc_final: 0.7603 (p0) REVERT: D 390 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: D 430 TYR cc_start: 0.8849 (m-80) cc_final: 0.8380 (m-80) REVERT: D 578 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8065 (t0) REVERT: D 662 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7730 (mm-30) REVERT: D 835 LYS cc_start: 0.8721 (tttp) cc_final: 0.8284 (ttpt) REVERT: E 106 LYS cc_start: 0.8879 (mtmm) cc_final: 0.8642 (ttmm) REVERT: E 191 ASN cc_start: 0.8225 (m-40) cc_final: 0.7399 (t0) REVERT: E 205 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: E 295 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7866 (mt-10) REVERT: E 763 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8360 (tmtt) REVERT: E 827 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8406 (mtmt) outliers start: 44 outliers final: 35 residues processed: 143 average time/residue: 0.1112 time to fit residues: 24.2057 Evaluate side-chains 148 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain D residue 848 VAL Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 763 LYS Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 17 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 789 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.101979 restraints weight = 23573.002| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.20 r_work: 0.3219 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14372 Z= 0.126 Angle : 0.534 8.202 19474 Z= 0.265 Chirality : 0.041 0.131 2012 Planarity : 0.004 0.052 2502 Dihedral : 9.409 179.931 1945 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 2.51 % Allowed : 21.91 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1694 helix: 1.06 (0.20), residues: 714 sheet: 0.77 (0.33), residues: 258 loop : -1.00 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 424 TYR 0.018 0.001 TYR D 696 PHE 0.016 0.001 PHE E 160 TRP 0.010 0.001 TRP E 40 HIS 0.004 0.001 HIS E 807 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14372) covalent geometry : angle 0.53363 / 0.26 (19474) hydrogen bonds : bond 0.03603 / 2.26 ( 625) hydrogen bonds : angle 4.46766 / 3.17 ( 1764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3388 Ramachandran restraints generated. 1694 Oldfield, 0 Emsley, 1694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: D 55 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8919 (tt) REVERT: D 159 TYR cc_start: 0.9092 (OUTLIER) cc_final: 0.8590 (t80) REVERT: D 306 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8908 (mp) REVERT: D 347 ASP cc_start: 0.8062 (t70) cc_final: 0.7459 (p0) REVERT: D 390 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8189 (mt0) REVERT: D 430 TYR cc_start: 0.8830 (m-80) cc_final: 0.8402 (m-80) REVERT: D 578 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7885 (t0) REVERT: D 662 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7666 (mm-30) REVERT: D 835 LYS cc_start: 0.8709 (tttp) cc_final: 0.8308 (ttpt) REVERT: E 166 MET cc_start: 0.6576 (mtp) cc_final: 0.6074 (mtt) REVERT: E 191 ASN cc_start: 0.8184 (m-40) cc_final: 0.7355 (t0) REVERT: E 250 LEU cc_start: 0.9172 (tp) cc_final: 0.8828 (tt) REVERT: E 295 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7825 (mt-10) REVERT: E 763 LYS cc_start: 0.8715 (tmmm) cc_final: 0.8397 (tmtt) REVERT: E 827 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8379 (mtmt) outliers start: 37 outliers final: 29 residues processed: 148 average time/residue: 0.1092 time to fit residues: 25.1330 Evaluate side-chains 147 residues out of total 1474 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 28 CYS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 159 TYR Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 302 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 390 GLN Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 606 SER Chi-restraints excluded: chain D residue 680 GLU Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 743 ASP Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 779 VAL Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 239 TYR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 617 ASN Chi-restraints excluded: chain E residue 747 VAL Chi-restraints excluded: chain E residue 754 MET Chi-restraints excluded: chain E residue 764 ILE Chi-restraints excluded: chain E residue 817 GLU Chi-restraints excluded: chain E residue 825 SER Chi-restraints excluded: chain E residue 827 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 789 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099586 restraints weight = 24337.906| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.31 r_work: 0.3149 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14372 Z= 0.148 Angle : 0.538 8.473 19474 Z= 0.267 Chirality : 0.041 0.133 2012 Planarity : 0.004 0.051 2502 Dihedral : 9.360 179.952 1945 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 2.51 % Allowed : 22.18 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1694 helix: 1.11 (0.20), residues: 713 sheet: 0.76 (0.33), residues: 260 loop : -0.97 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 424 TYR 0.022 0.001 TYR D 696 PHE 0.016 0.001 PHE E 160 TRP 0.010 0.001 TRP D 40 HIS 0.004 0.001 HIS E 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14372) covalent geometry : angle 0.53807 / 0.27 (19474) hydrogen bonds : bond 0.03702 / 2.32 ( 625) hydrogen bonds : angle 4.48036 / 3.18 ( 1764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.53 seconds wall clock time: 62 minutes 16.12 seconds (3736.12 seconds total)