Starting phenix.real_space_refine on Sat Aug 8 05:02:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2026/8hwb_35052.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s 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: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "F" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.23, per 1000 atoms: 0.20 Number of scatterers: 25740 At special positions: 0 Unit cell: (130.305, 127.02, 175.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 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: 1.82 Conformation dependent library (CDL) restraints added in 1.1 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 45 sheets defined 42.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.405A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 489 through 491 No H-bonds generated for 'chain 'A' and resid 489 through 491' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 528 through 532 removed outlier: 4.126A pdb=" N ILE A 531 " --> pdb=" O GLY A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 570 through 578 removed outlier: 3.659A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.106A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.515A pdb=" N PHE A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 429 through 435 removed outlier: 4.082A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.715A pdb=" N LYS B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 475 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.633A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.727A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.955A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.568A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 700 removed outlier: 3.592A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 4.048A pdb=" N ASN C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.703A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 398 Processing helix chain 'C' and resid 429 through 435 removed outlier: 4.377A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 528 through 532 removed outlier: 3.989A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.513A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.799A pdb=" N ARG C 619 " --> pdb=" O ASN C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 634 No H-bonds generated for 'chain 'C' and resid 632 through 634' Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.403A pdb=" N GLY C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 removed outlier: 3.538A pdb=" N PHE C 668 " --> pdb=" O TYR C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.826A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 699 removed outlier: 3.654A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.714A pdb=" N GLN D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 removed outlier: 3.560A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 104 removed outlier: 3.504A pdb=" N GLN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 4.441A pdb=" N ASN D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 160 removed outlier: 4.450A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.086A pdb=" N LEU D 208 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.763A pdb=" N CYS D 314 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.578A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.636A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 398 removed outlier: 3.514A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 removed outlier: 4.159A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 472 through 474 No H-bonds generated for 'chain 'D' and resid 472 through 474' Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 528 through 532 removed outlier: 3.866A pdb=" N ILE D 531 " --> pdb=" O GLY D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 576 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.621A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 654 through 659 Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 removed outlier: 4.020A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 700 removed outlier: 3.816A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.732A pdb=" N ARG E 24 " --> pdb=" O PRO E 20 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLN E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 20 through 25' Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 78 through 105 Processing helix chain 'E' and resid 108 through 119 removed outlier: 4.279A pdb=" N ASN E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 150 through 160 Processing helix chain 'E' and resid 163 through 168 Processing helix chain 'E' and resid 203 through 208 removed outlier: 3.830A pdb=" N LEU E 208 " --> pdb=" O GLU E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 230 removed outlier: 3.714A pdb=" N LEU E 230 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 254 removed outlier: 3.561A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE E 254 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.725A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 3.942A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 398 removed outlier: 3.513A pdb=" N ARG E 389 " --> pdb=" O CYS E 385 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 removed outlier: 4.078A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.665A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 removed outlier: 3.516A pdb=" N ARG E 479 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 528 through 533 removed outlier: 4.323A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.571A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.503A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 642 Processing helix chain 'E' and resid 654 through 659 Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.538A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 4.008A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 698 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.841A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 381 removed outlier: 3.850A pdb=" N SER F 380 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 376 through 381' Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.516A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.772A pdb=" N ASP F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 removed outlier: 3.953A pdb=" N GLU F 459 " --> pdb=" O SER F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 removed outlier: 3.508A pdb=" N ARG F 479 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.917A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.731A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 699 removed outlier: 3.514A pdb=" N ALA F 697 " --> pdb=" O ILE F 693 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 removed outlier: 3.505A pdb=" N GLY K 7 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 26 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 78 through 104 removed outlier: 3.508A pdb=" N ASP K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.511A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 150 Processing helix chain 'K' and resid 150 through 160 Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 203 through 208 removed outlier: 4.208A pdb=" N LEU K 208 " --> pdb=" O GLU K 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 340 through 341 Processing sheet with id=AA2, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.657A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.511A pdb=" N VAL A 553 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP A 603 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N CYS A 555 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 582 through 583 removed outlier: 3.778A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 631 Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.961A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.899A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AB2, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB3, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.916A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 419 " --> pdb=" O TYR C 428 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.685A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR C 499 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.750A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.744A pdb=" N PHE D 12 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 64 through 73 removed outlier: 11.026A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER D 132 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS D 134 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR D 123 " --> pdb=" O HIS D 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 64 through 73 removed outlier: 11.026A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.694A pdb=" N LYS D 317 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AC3, first strand: chain 'D' and resid 412 through 415 removed outlier: 4.002A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 419 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 525 through 526 removed outlier: 6.856A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC6, first strand: chain 'D' and resid 629 through 631 Processing sheet with id=AC7, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.557A pdb=" N GLU E 33 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE E 12 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.981A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 64 through 73 removed outlier: 10.981A pdb=" N VAL E 65 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N ASP E 139 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE E 67 " --> pdb=" O PHE E 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.572A pdb=" N LYS E 124 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AD4, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AD5, first strand: chain 'E' and resid 339 through 341 removed outlier: 3.520A pdb=" N LYS E 356 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 351 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.644A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL E 419 " --> pdb=" O TYR E 428 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.752A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 553 " --> pdb=" O ILE E 601 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ASP E 603 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N CYS E 555 " --> pdb=" O ASP E 603 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AD9, first strand: chain 'E' and resid 629 through 631 removed outlier: 7.001A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 340 through 341 removed outlier: 3.578A pdb=" N LEU F 340 " --> pdb=" O ILE F 348 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 412 through 415 Processing sheet with id=AE3, first strand: chain 'F' and resid 525 through 527 removed outlier: 3.596A pdb=" N PHE F 554 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.437A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.587A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL K 13 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE K 12 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 64 through 68 removed outlier: 7.099A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 64 through 68 removed outlier: 7.099A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 71 through 73 removed outlier: 3.544A pdb=" N PHE K 133 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 124 through 125 removed outlier: 3.517A pdb=" N LYS K 124 " --> pdb=" O VAL K 196 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2400 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: 4.78 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6639 1.33 - 1.45: 4767 1.45 - 1.58: 14628 1.58 - 1.70: 40 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" C1' DT S 4 " pdb=" N1 DT S 4 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.44e+00 bond pdb=" C1' DT S 3 " pdb=" N1 DT S 3 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.27e+00 bond pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 1.435 1.468 -0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" C GLU D 237 " pdb=" N PRO D 238 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.26e-02 6.30e+03 6.07e+00 bond pdb=" N LEU A 577 " pdb=" CA LEU A 577 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.35e-02 5.49e+03 6.03e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 35137 2.38 - 4.76: 407 4.76 - 7.14: 40 7.14 - 9.51: 6 9.51 - 11.89: 3 Bond angle restraints: 35593 Sorted by residual: angle pdb=" CA PRO E 29 " pdb=" N PRO E 29 " pdb=" CD PRO E 29 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" N3 DT S 6 " pdb=" C4 DT S 6 " pdb=" O4 DT S 6 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N LEU F 700 " pdb=" CA LEU F 700 " pdb=" C LEU F 700 " ideal model delta sigma weight residual 113.50 108.43 5.07 1.23e+00 6.61e-01 1.70e+01 angle pdb=" N3 DT S 4 " pdb=" C4 DT S 4 " pdb=" O4 DT S 4 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT S 5 " pdb=" C4 DT S 5 " pdb=" O4 DT S 5 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.64e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 15412 31.41 - 62.82: 670 62.82 - 94.23: 44 94.23 - 125.64: 1 125.64 - 157.05: 2 Dihedral angle restraints: 16129 sinusoidal: 6838 harmonic: 9291 Sorted by residual: dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 62.95 157.05 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.88 152.12 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " pdb=" OD1 ASP A 335 " ideal model delta sinusoidal sigma weight residual -30.00 -90.06 60.06 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2681 0.038 - 0.076: 948 0.076 - 0.113: 313 0.113 - 0.151: 36 0.151 - 0.189: 6 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU A 700 " pdb=" N LEU A 700 " pdb=" C LEU A 700 " pdb=" CB LEU A 700 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA LEU A 577 " pdb=" N LEU A 577 " pdb=" C LEU A 577 " pdb=" CB LEU A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 28 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO E 29 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 455 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.49e+01 pdb=" N PRO F 456 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO F 456 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 456 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 300 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ASN E 300 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN E 300 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY E 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 191 2.50 - 3.10: 18496 3.10 - 3.70: 38565 3.70 - 4.30: 52984 4.30 - 4.90: 88127 Nonbonded interactions: 198363 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.900 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 1.937 2.170 nonbonded pdb=" O3G ATP C1001 " pdb="MG MG C1002 " model vdw 1.971 2.170 nonbonded pdb=" O2B ATP B1001 " pdb="MG MG B1002 " model vdw 1.991 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.013 2.170 ... (remaining 198358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 323 through 701) selection = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = chain 'F' } ncs_group { reference = (chain 'D' and resid 1 through 700) selection = (chain 'E' and resid 1 through 700) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.720 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 26281 Z= 0.163 Angle : 0.637 11.893 35593 Z= 0.367 Chirality : 0.042 0.189 3984 Planarity : 0.004 0.108 4537 Dihedral : 16.504 157.050 10087 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 0.59 % Allowed : 18.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.13 (0.15), residues: 3133 helix: 0.54 (0.17), residues: 1040 sheet: -1.30 (0.25), residues: 452 loop : -1.44 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 159 TYR 0.019 0.001 TYR F 645 PHE 0.015 0.001 PHE E 240 TRP 0.011 0.001 TRP A 675 HIS 0.014 0.001 HIS F 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (26281) covalent geometry : angle 0.63700 / 0.37 (35593) hydrogen bonds : bond 0.22460 / 14.80 ( 852) hydrogen bonds : angle 7.10244 / 4.87 ( 2400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7815 (mmm) cc_final: 0.7591 (tpp) REVERT: A 593 ASN cc_start: 0.8654 (m-40) cc_final: 0.8288 (t0) REVERT: A 618 MET cc_start: 0.7102 (ptp) cc_final: 0.6864 (pmm) REVERT: D 1 MET cc_start: 0.3721 (ttt) cc_final: 0.3517 (ttt) REVERT: E 116 MET cc_start: 0.7572 (ptp) cc_final: 0.7011 (ppp) REVERT: E 223 LEU cc_start: 0.8394 (mm) cc_final: 0.8129 (tp) REVERT: E 455 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7306 (t) outliers start: 17 outliers final: 5 residues processed: 240 average time/residue: 0.1500 time to fit residues: 58.6994 Evaluate side-chains 215 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0570 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 2.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 662 ASN B 466 ASN ** E 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN E 573 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 629 HIS F 641 ASN K 195 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.072085 restraints weight = 72234.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.074107 restraints weight = 41807.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075408 restraints weight = 29376.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.076244 restraints weight = 23444.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.076767 restraints weight = 20300.841| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 26281 Z= 0.221 Angle : 0.627 8.958 35593 Z= 0.325 Chirality : 0.045 0.340 3984 Planarity : 0.004 0.078 4537 Dihedral : 10.331 156.305 3679 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.66 % Favored : 95.31 % Rotamer: Outliers : 2.50 % Allowed : 17.38 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.19 (0.15), residues: 3133 helix: 0.47 (0.16), residues: 1082 sheet: -1.41 (0.24), residues: 466 loop : -1.49 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 389 TYR 0.022 0.001 TYR A 482 PHE 0.017 0.002 PHE E 240 TRP 0.012 0.001 TRP D 350 HIS 0.009 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (26281) covalent geometry : angle 0.62676 / 0.32 (35593) hydrogen bonds : bond 0.04701 / 3.12 ( 852) hydrogen bonds : angle 5.35663 / 3.71 ( 2400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 210 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.6563 (t0) cc_final: 0.6348 (t0) REVERT: A 593 ASN cc_start: 0.8766 (m-40) cc_final: 0.8339 (t0) REVERT: A 618 MET cc_start: 0.7349 (ptp) cc_final: 0.6879 (pmm) REVERT: A 684 MET cc_start: 0.5334 (tpt) cc_final: 0.4892 (tpt) REVERT: D 150 MET cc_start: 0.7930 (mmm) cc_final: 0.7592 (mmm) REVERT: D 377 LYS cc_start: 0.8653 (tptt) cc_final: 0.8257 (tptm) REVERT: D 382 GLU cc_start: 0.8420 (tp30) cc_final: 0.8113 (tp30) REVERT: D 462 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8245 (mmm) REVERT: E 223 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8260 (tp) REVERT: E 300 ASN cc_start: 0.8369 (t0) cc_final: 0.8030 (t0) REVERT: E 455 SER cc_start: 0.6901 (OUTLIER) cc_final: 0.5528 (t) REVERT: E 618 MET cc_start: 0.7787 (mtm) cc_final: 0.7389 (mtm) REVERT: K 104 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7959 (mm-30) outliers start: 72 outliers final: 42 residues processed: 265 average time/residue: 0.1292 time to fit residues: 57.9429 Evaluate side-chains 231 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 621 ILE Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.073449 restraints weight = 72054.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075505 restraints weight = 41562.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076817 restraints weight = 29122.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077691 restraints weight = 23263.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.078224 restraints weight = 20121.807| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 26281 Z= 0.123 Angle : 0.536 9.117 35593 Z= 0.278 Chirality : 0.043 0.331 3984 Planarity : 0.004 0.070 4537 Dihedral : 9.890 154.494 3677 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.54 % Favored : 96.43 % Rotamer: Outliers : 2.43 % Allowed : 18.00 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.97 (0.15), residues: 3133 helix: 0.71 (0.16), residues: 1074 sheet: -1.26 (0.24), residues: 479 loop : -1.40 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 389 TYR 0.016 0.001 TYR A 482 PHE 0.017 0.001 PHE F 543 TRP 0.011 0.001 TRP C 350 HIS 0.015 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (26281) covalent geometry : angle 0.53618 / 0.28 (35593) hydrogen bonds : bond 0.03717 / 2.44 ( 852) hydrogen bonds : angle 4.80447 / 3.34 ( 2400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 211 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8357 (mmm) cc_final: 0.8148 (mmm) REVERT: A 534 ASP cc_start: 0.6669 (t70) cc_final: 0.6388 (t0) REVERT: A 593 ASN cc_start: 0.8797 (m-40) cc_final: 0.8404 (t0) REVERT: D 62 TYR cc_start: 0.6886 (m-80) cc_final: 0.6671 (m-80) REVERT: D 150 MET cc_start: 0.7919 (mmm) cc_final: 0.7572 (mmm) REVERT: D 377 LYS cc_start: 0.8671 (tptt) cc_final: 0.8256 (tptm) REVERT: D 382 GLU cc_start: 0.8398 (tp30) cc_final: 0.8175 (tp30) REVERT: E 116 MET cc_start: 0.7884 (ptp) cc_final: 0.7448 (ppp) REVERT: E 223 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8278 (tp) REVERT: E 300 ASN cc_start: 0.8263 (t0) cc_final: 0.7899 (t0) REVERT: E 618 MET cc_start: 0.7867 (mtm) cc_final: 0.7450 (mtm) outliers start: 70 outliers final: 43 residues processed: 260 average time/residue: 0.1309 time to fit residues: 58.2214 Evaluate side-chains 235 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain K residue 135 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 10.0000 chunk 264 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 150 optimal weight: 0.9990 chunk 279 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 597 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN F 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074304 restraints weight = 71066.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076368 restraints weight = 40952.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077718 restraints weight = 28611.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.078545 restraints weight = 22734.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079095 restraints weight = 19708.674| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 26281 Z= 0.102 Angle : 0.514 8.866 35593 Z= 0.264 Chirality : 0.042 0.329 3984 Planarity : 0.004 0.067 4537 Dihedral : 9.591 154.480 3676 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer: Outliers : 2.39 % Allowed : 18.42 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.79 (0.15), residues: 3133 helix: 0.89 (0.16), residues: 1064 sheet: -1.10 (0.24), residues: 469 loop : -1.32 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 24 TYR 0.014 0.001 TYR B 482 PHE 0.015 0.001 PHE F 543 TRP 0.008 0.001 TRP C 350 HIS 0.006 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (26281) covalent geometry : angle 0.51366 / 0.26 (35593) hydrogen bonds : bond 0.03173 / 2.08 ( 852) hydrogen bonds : angle 4.50825 / 3.13 ( 2400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 224 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8398 (mmm) cc_final: 0.8183 (mmm) REVERT: A 534 ASP cc_start: 0.6694 (t70) cc_final: 0.6381 (t0) REVERT: A 593 ASN cc_start: 0.8756 (m-40) cc_final: 0.8336 (t0) REVERT: A 656 ASP cc_start: 0.8888 (p0) cc_final: 0.8529 (t0) REVERT: D 62 TYR cc_start: 0.6863 (m-80) cc_final: 0.6662 (m-80) REVERT: D 110 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8182 (tp30) REVERT: D 150 MET cc_start: 0.8050 (mmm) cc_final: 0.7581 (mmm) REVERT: D 377 LYS cc_start: 0.8563 (tptt) cc_final: 0.8180 (tptm) REVERT: D 462 MET cc_start: 0.8700 (mmm) cc_final: 0.8312 (tpt) REVERT: D 684 MET cc_start: 0.8658 (ttp) cc_final: 0.8288 (ttp) REVERT: E 116 MET cc_start: 0.7962 (ptp) cc_final: 0.7549 (ppp) REVERT: E 223 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8267 (tp) REVERT: E 290 HIS cc_start: 0.5615 (m-70) cc_final: 0.5382 (m170) REVERT: E 300 ASN cc_start: 0.8269 (t0) cc_final: 0.7940 (t0) REVERT: E 455 SER cc_start: 0.7195 (OUTLIER) cc_final: 0.6418 (t) REVERT: E 618 MET cc_start: 0.7883 (mtm) cc_final: 0.7491 (mtm) REVERT: K 116 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7441 (mtm) outliers start: 69 outliers final: 41 residues processed: 275 average time/residue: 0.1316 time to fit residues: 61.0078 Evaluate side-chains 238 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 700 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 36 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 147 optimal weight: 0.4980 chunk 175 optimal weight: 4.9990 chunk 228 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 593 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.103462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074810 restraints weight = 71530.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.076866 restraints weight = 41300.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078229 restraints weight = 28883.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.079062 restraints weight = 22975.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.079553 restraints weight = 19918.658| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 26281 Z= 0.097 Angle : 0.516 9.287 35593 Z= 0.263 Chirality : 0.042 0.330 3984 Planarity : 0.004 0.064 4537 Dihedral : 9.333 154.290 3673 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 18.66 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.70 (0.15), residues: 3133 helix: 0.98 (0.16), residues: 1064 sheet: -1.04 (0.24), residues: 469 loop : -1.28 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 389 TYR 0.013 0.001 TYR B 482 PHE 0.015 0.001 PHE F 610 TRP 0.007 0.001 TRP C 350 HIS 0.005 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (26281) covalent geometry : angle 0.51597 / 0.26 (35593) hydrogen bonds : bond 0.02989 / 1.96 ( 852) hydrogen bonds : angle 4.34595 / 3.03 ( 2400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 216 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9521 (tp) cc_final: 0.9293 (tp) REVERT: A 462 MET cc_start: 0.8406 (mmm) cc_final: 0.8197 (mmm) REVERT: A 534 ASP cc_start: 0.6681 (t70) cc_final: 0.6323 (t0) REVERT: A 593 ASN cc_start: 0.8761 (m-40) cc_final: 0.8244 (t0) REVERT: A 618 MET cc_start: 0.7212 (pmm) cc_final: 0.6965 (pmm) REVERT: A 656 ASP cc_start: 0.8834 (p0) cc_final: 0.8520 (t0) REVERT: D 62 TYR cc_start: 0.6892 (m-80) cc_final: 0.6681 (m-80) REVERT: D 110 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8206 (tp30) REVERT: D 150 MET cc_start: 0.8051 (mmm) cc_final: 0.7663 (mmm) REVERT: E 116 MET cc_start: 0.7894 (ptp) cc_final: 0.7541 (ppp) REVERT: E 170 ASP cc_start: 0.7796 (t0) cc_final: 0.7049 (p0) REVERT: E 223 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8268 (tp) REVERT: E 290 HIS cc_start: 0.5584 (m-70) cc_final: 0.5343 (m170) REVERT: E 300 ASN cc_start: 0.8207 (t0) cc_final: 0.7767 (t0) REVERT: E 618 MET cc_start: 0.7874 (mtm) cc_final: 0.7460 (mtm) REVERT: F 501 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8281 (m-10) REVERT: K 104 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7745 (mm-30) outliers start: 74 outliers final: 52 residues processed: 267 average time/residue: 0.1367 time to fit residues: 61.7495 Evaluate side-chains 254 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 200 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 377 LYS Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 501 PHE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 37 CYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 229 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 303 optimal weight: 0.9980 chunk 203 optimal weight: 10.0000 chunk 296 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 246 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.072052 restraints weight = 71983.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.074078 restraints weight = 41541.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.075391 restraints weight = 29197.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.076221 restraints weight = 23319.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076732 restraints weight = 20264.642| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26281 Z= 0.170 Angle : 0.577 11.627 35593 Z= 0.293 Chirality : 0.043 0.342 3984 Planarity : 0.004 0.066 4537 Dihedral : 9.383 154.866 3673 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.04 % Favored : 94.92 % Rotamer: Outliers : 2.81 % Allowed : 19.01 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.75 (0.15), residues: 3133 helix: 0.94 (0.16), residues: 1089 sheet: -1.14 (0.24), residues: 478 loop : -1.33 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 389 TYR 0.020 0.001 TYR A 482 PHE 0.015 0.001 PHE E 240 TRP 0.011 0.001 TRP D 350 HIS 0.005 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (26281) covalent geometry : angle 0.57683 / 0.29 (35593) hydrogen bonds : bond 0.03509 / 2.34 ( 852) hydrogen bonds : angle 4.52288 / 3.14 ( 2400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 208 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8531 (mmm) cc_final: 0.8290 (mmm) REVERT: A 529 GLN cc_start: 0.8679 (mm-40) cc_final: 0.7914 (mp10) REVERT: A 593 ASN cc_start: 0.8847 (m-40) cc_final: 0.8338 (t0) REVERT: A 618 MET cc_start: 0.7183 (pmm) cc_final: 0.6924 (pmm) REVERT: A 656 ASP cc_start: 0.8873 (p0) cc_final: 0.8579 (t0) REVERT: D 110 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8239 (tp30) REVERT: D 150 MET cc_start: 0.7851 (mmm) cc_final: 0.7480 (mmm) REVERT: D 377 LYS cc_start: 0.8444 (tptm) cc_final: 0.8083 (tptm) REVERT: D 462 MET cc_start: 0.8767 (mmm) cc_final: 0.8342 (tpt) REVERT: E 116 MET cc_start: 0.8025 (ptp) cc_final: 0.7697 (ppp) REVERT: E 223 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8287 (tp) REVERT: E 300 ASN cc_start: 0.8206 (t0) cc_final: 0.7766 (t0) REVERT: E 455 SER cc_start: 0.7373 (OUTLIER) cc_final: 0.6980 (t) REVERT: E 618 MET cc_start: 0.7992 (mtm) cc_final: 0.7533 (mtm) REVERT: F 632 GLN cc_start: 0.2093 (OUTLIER) cc_final: 0.1446 (mp-120) REVERT: F 682 PRO cc_start: 0.7973 (Cg_endo) cc_final: 0.7733 (Cg_exo) outliers start: 81 outliers final: 63 residues processed: 268 average time/residue: 0.1256 time to fit residues: 57.1415 Evaluate side-chains 253 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 187 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 426 MET Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 37 CYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 94 optimal weight: 0.7980 chunk 281 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 268 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 548 HIS F 347 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.071811 restraints weight = 72866.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073878 restraints weight = 41361.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.075228 restraints weight = 28822.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.076093 restraints weight = 22843.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076539 restraints weight = 19746.241| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26281 Z= 0.154 Angle : 0.569 12.388 35593 Z= 0.288 Chirality : 0.043 0.345 3984 Planarity : 0.004 0.062 4537 Dihedral : 9.331 153.891 3673 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 3.05 % Allowed : 19.46 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.72 (0.15), residues: 3133 helix: 0.89 (0.16), residues: 1107 sheet: -1.14 (0.24), residues: 495 loop : -1.26 (0.15), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 389 TYR 0.019 0.001 TYR A 482 PHE 0.016 0.001 PHE D 68 TRP 0.010 0.001 TRP C 350 HIS 0.005 0.001 HIS F 548 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (26281) covalent geometry : angle 0.56910 / 0.29 (35593) hydrogen bonds : bond 0.03263 / 2.17 ( 852) hydrogen bonds : angle 4.47410 / 3.11 ( 2400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 197 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8620 (mmm) cc_final: 0.8397 (mmm) REVERT: A 529 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8429 (mp10) REVERT: A 593 ASN cc_start: 0.8902 (m-40) cc_final: 0.8409 (t0) REVERT: A 618 MET cc_start: 0.7157 (pmm) cc_final: 0.6892 (pmm) REVERT: A 656 ASP cc_start: 0.8840 (p0) cc_final: 0.8569 (t0) REVERT: B 615 ASN cc_start: 0.8804 (t0) cc_final: 0.8459 (p0) REVERT: B 618 MET cc_start: 0.7596 (mtm) cc_final: 0.7256 (mtm) REVERT: C 450 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8264 (mttp) REVERT: D 56 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8351 (tt) REVERT: D 110 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8243 (tp30) REVERT: D 150 MET cc_start: 0.7585 (mmm) cc_final: 0.7331 (mmm) REVERT: D 377 LYS cc_start: 0.8450 (tptm) cc_final: 0.8176 (tptm) REVERT: E 116 MET cc_start: 0.8097 (ptp) cc_final: 0.7787 (ppp) REVERT: E 223 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8288 (tp) REVERT: E 300 ASN cc_start: 0.8239 (t0) cc_final: 0.7985 (t0) REVERT: E 618 MET cc_start: 0.8014 (mtm) cc_final: 0.7533 (mtm) REVERT: F 632 GLN cc_start: 0.1992 (OUTLIER) cc_final: 0.1366 (mp-120) REVERT: F 682 PRO cc_start: 0.7971 (Cg_endo) cc_final: 0.7757 (Cg_exo) REVERT: K 1 MET cc_start: 0.2699 (tpp) cc_final: 0.2240 (tpp) outliers start: 88 outliers final: 70 residues processed: 263 average time/residue: 0.1261 time to fit residues: 56.7143 Evaluate side-chains 263 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 190 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 257 optimal weight: 0.0970 chunk 39 optimal weight: 2.9990 chunk 238 optimal weight: 0.4980 chunk 284 optimal weight: 0.5980 chunk 159 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 chunk 139 optimal weight: 0.0060 chunk 43 optimal weight: 0.8980 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 353 ASN E 201 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.074778 restraints weight = 72875.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076820 restraints weight = 42173.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.078150 restraints weight = 29556.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078996 restraints weight = 23535.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.079507 restraints weight = 20358.105| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 26281 Z= 0.095 Angle : 0.534 11.142 35593 Z= 0.270 Chirality : 0.042 0.334 3984 Planarity : 0.003 0.058 4537 Dihedral : 9.082 153.658 3671 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 20.40 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.56 (0.15), residues: 3133 helix: 1.06 (0.16), residues: 1092 sheet: -1.04 (0.24), residues: 494 loop : -1.17 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 117 TYR 0.012 0.001 TYR B 482 PHE 0.017 0.001 PHE F 543 TRP 0.010 0.001 TRP C 350 HIS 0.003 0.001 HIS C 680 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (26281) covalent geometry : angle 0.53420 / 0.27 (35593) hydrogen bonds : bond 0.02797 / 1.83 ( 852) hydrogen bonds : angle 4.16980 / 2.90 ( 2400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 216 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9530 (tp) cc_final: 0.9316 (tp) REVERT: A 529 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8389 (mp10) REVERT: A 593 ASN cc_start: 0.8829 (m-40) cc_final: 0.8308 (t0) REVERT: A 618 MET cc_start: 0.7187 (pmm) cc_final: 0.6893 (pmm) REVERT: B 615 ASN cc_start: 0.8648 (t0) cc_final: 0.8425 (p0) REVERT: B 618 MET cc_start: 0.7483 (mtm) cc_final: 0.7165 (mtm) REVERT: D 110 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8225 (tp30) REVERT: D 116 MET cc_start: 0.7773 (ttp) cc_final: 0.7375 (ppp) REVERT: D 150 MET cc_start: 0.7702 (mmm) cc_final: 0.7442 (mmm) REVERT: D 377 LYS cc_start: 0.8377 (tptm) cc_final: 0.8052 (tptm) REVERT: E 116 MET cc_start: 0.8290 (ptp) cc_final: 0.8061 (ppp) REVERT: E 170 ASP cc_start: 0.7929 (t0) cc_final: 0.6708 (p0) REVERT: E 214 MET cc_start: 0.3746 (mtm) cc_final: 0.3322 (tpt) REVERT: E 223 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8219 (tp) REVERT: E 300 ASN cc_start: 0.8206 (t0) cc_final: 0.7834 (t0) REVERT: E 618 MET cc_start: 0.7891 (mtm) cc_final: 0.7449 (mtm) REVERT: F 444 PHE cc_start: 0.6916 (p90) cc_final: 0.6679 (p90) REVERT: F 632 GLN cc_start: 0.1940 (OUTLIER) cc_final: 0.1261 (mp-120) REVERT: F 682 PRO cc_start: 0.7878 (Cg_endo) cc_final: 0.7652 (Cg_exo) REVERT: K 1 MET cc_start: 0.2865 (tpp) cc_final: 0.2460 (tpp) outliers start: 66 outliers final: 53 residues processed: 265 average time/residue: 0.1274 time to fit residues: 57.3162 Evaluate side-chains 250 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 55 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 259 optimal weight: 0.0270 chunk 15 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 328 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.072310 restraints weight = 72217.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074296 restraints weight = 41794.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075617 restraints weight = 29527.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076446 restraints weight = 23584.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076891 restraints weight = 20512.250| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26281 Z= 0.149 Angle : 0.573 12.272 35593 Z= 0.289 Chirality : 0.043 0.343 3984 Planarity : 0.004 0.060 4537 Dihedral : 9.106 154.565 3671 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 2.46 % Allowed : 20.64 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.56 (0.15), residues: 3133 helix: 1.02 (0.16), residues: 1109 sheet: -1.02 (0.24), residues: 494 loop : -1.17 (0.16), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 152 TYR 0.018 0.001 TYR A 482 PHE 0.016 0.001 PHE F 543 TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS K 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (26281) covalent geometry : angle 0.57271 / 0.29 (35593) hydrogen bonds : bond 0.03220 / 2.14 ( 852) hydrogen bonds : angle 4.34594 / 3.02 ( 2400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 198 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8521 (mp10) REVERT: A 593 ASN cc_start: 0.8884 (m-40) cc_final: 0.8384 (t0) REVERT: B 615 ASN cc_start: 0.8727 (t0) cc_final: 0.8443 (p0) REVERT: B 618 MET cc_start: 0.7559 (mtm) cc_final: 0.7132 (mtm) REVERT: D 110 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8214 (tp30) REVERT: D 116 MET cc_start: 0.7869 (ttp) cc_final: 0.7361 (ppp) REVERT: D 150 MET cc_start: 0.7668 (mmm) cc_final: 0.7443 (mmm) REVERT: D 377 LYS cc_start: 0.8404 (tptm) cc_final: 0.8125 (tptm) REVERT: D 462 MET cc_start: 0.8786 (mmm) cc_final: 0.8372 (tpt) REVERT: E 116 MET cc_start: 0.8344 (ptp) cc_final: 0.8058 (ppp) REVERT: E 170 ASP cc_start: 0.7940 (t0) cc_final: 0.6964 (p0) REVERT: E 214 MET cc_start: 0.3934 (mtm) cc_final: 0.3440 (tpt) REVERT: E 223 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8255 (tp) REVERT: E 300 ASN cc_start: 0.8268 (t0) cc_final: 0.7917 (t0) REVERT: E 618 MET cc_start: 0.8009 (mtm) cc_final: 0.7593 (mtm) REVERT: F 444 PHE cc_start: 0.6990 (p90) cc_final: 0.6786 (p90) REVERT: F 632 GLN cc_start: 0.2009 (OUTLIER) cc_final: 0.1354 (mp-120) REVERT: K 1 MET cc_start: 0.2736 (tpp) cc_final: 0.2287 (tpp) outliers start: 71 outliers final: 56 residues processed: 252 average time/residue: 0.1236 time to fit residues: 53.2409 Evaluate side-chains 248 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 190 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain K residue 37 CYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 128 optimal weight: 0.9980 chunk 193 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 274 optimal weight: 7.9990 chunk 252 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 463 ASN C 593 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.070774 restraints weight = 72287.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072881 restraints weight = 40407.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074262 restraints weight = 27987.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075123 restraints weight = 22115.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075572 restraints weight = 19086.263| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26281 Z= 0.181 Angle : 0.613 12.088 35593 Z= 0.309 Chirality : 0.044 0.352 3984 Planarity : 0.004 0.061 4537 Dihedral : 9.208 154.152 3671 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.23 % Favored : 94.73 % Rotamer: Outliers : 2.32 % Allowed : 20.78 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.72 (0.15), residues: 3133 helix: 0.89 (0.16), residues: 1112 sheet: -1.13 (0.25), residues: 457 loop : -1.28 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 152 TYR 0.022 0.001 TYR A 482 PHE 0.018 0.001 PHE F 543 TRP 0.013 0.001 TRP D 350 HIS 0.006 0.001 HIS C 373 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (26281) covalent geometry : angle 0.61274 / 0.31 (35593) hydrogen bonds : bond 0.03547 / 2.35 ( 852) hydrogen bonds : angle 4.54739 / 3.16 ( 2400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8685 (mp10) REVERT: A 593 ASN cc_start: 0.8934 (m-40) cc_final: 0.8496 (t0) REVERT: B 615 ASN cc_start: 0.8818 (t0) cc_final: 0.8478 (p0) REVERT: B 618 MET cc_start: 0.7625 (mtm) cc_final: 0.7234 (mtm) REVERT: C 696 PHE cc_start: 0.7881 (m-80) cc_final: 0.7674 (m-80) REVERT: D 110 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8206 (tp30) REVERT: D 150 MET cc_start: 0.7533 (mmm) cc_final: 0.7180 (mmm) REVERT: D 377 LYS cc_start: 0.8473 (tptm) cc_final: 0.8243 (tptm) REVERT: D 462 MET cc_start: 0.8763 (mmm) cc_final: 0.8370 (tpt) REVERT: D 522 ASP cc_start: 0.8347 (t70) cc_final: 0.8024 (t0) REVERT: E 116 MET cc_start: 0.8393 (ptp) cc_final: 0.8079 (ppp) REVERT: E 214 MET cc_start: 0.4149 (mtm) cc_final: 0.3670 (tpt) REVERT: E 300 ASN cc_start: 0.8290 (t0) cc_final: 0.8008 (t0) REVERT: E 618 MET cc_start: 0.8041 (mtm) cc_final: 0.7609 (mtm) REVERT: F 444 PHE cc_start: 0.7015 (p90) cc_final: 0.6682 (p90) REVERT: F 632 GLN cc_start: 0.1931 (OUTLIER) cc_final: 0.1303 (mp-120) REVERT: K 1 MET cc_start: 0.2775 (tpp) cc_final: 0.2324 (tpp) outliers start: 67 outliers final: 63 residues processed: 239 average time/residue: 0.1294 time to fit residues: 53.3611 Evaluate side-chains 247 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 183 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 385 CYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 37 CYS Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 160 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 295 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 278 optimal weight: 0.0970 chunk 33 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.101449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.074018 restraints weight = 71998.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.076237 restraints weight = 43489.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.076484 restraints weight = 29430.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.076945 restraints weight = 26074.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.076989 restraints weight = 23491.437| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 26281 Z= 0.108 Angle : 0.562 12.376 35593 Z= 0.283 Chirality : 0.042 0.339 3984 Planarity : 0.004 0.062 4537 Dihedral : 9.030 153.515 3671 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 1.98 % Allowed : 21.30 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.59 (0.15), residues: 3133 helix: 0.98 (0.16), residues: 1109 sheet: -1.04 (0.25), residues: 460 loop : -1.18 (0.15), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 152 TYR 0.014 0.001 TYR B 482 PHE 0.014 0.001 PHE F 543 TRP 0.010 0.001 TRP C 350 HIS 0.003 0.000 HIS D 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (26281) covalent geometry : angle 0.56177 / 0.28 (35593) hydrogen bonds : bond 0.02924 / 1.92 ( 852) hydrogen bonds : angle 4.23736 / 2.94 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3339.66 seconds wall clock time: 59 minutes 2.51 seconds (3542.51 seconds total)