Starting phenix.real_space_refine on Mon Aug 25 07:06:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwb_35052/08_2025/8hwb_35052.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwb_35052/08_2025/8hwb_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_2025/8hwb_35052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2025/8hwb_35052.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2025/8hwb_35052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwb_35052/08_2025/8hwb_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-2.0-5787/lib/python3.9/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: 4.96, per 1000 atoms: 0.19 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: 1.69 Conformation dependent library (CDL) restraints added in 828.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 3.38 Time building geometry restraints manager: 2.16 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=" 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 bond pdb=" N LEU E 321 " pdb=" CA LEU E 321 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N SER K 160 " pdb=" CA SER K 160 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.50e+00 bond pdb=" N LEU C 700 " pdb=" CA LEU C 700 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 35150 2.38 - 4.76: 394 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=" 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=" CA GLU D 382 " pdb=" CB GLU D 382 " pdb=" CG GLU D 382 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N PHE B 698 " pdb=" CA PHE B 698 " pdb=" C PHE B 698 " ideal model delta sigma weight residual 112.23 107.20 5.03 1.26e+00 6.30e-01 1.60e+01 angle pdb=" N MET F 458 " pdb=" CA MET F 458 " pdb=" CB MET F 458 " ideal model delta sigma weight residual 110.01 115.80 -5.79 1.45e+00 4.76e-01 1.59e+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: 2683 0.038 - 0.076: 949 0.076 - 0.113: 313 0.113 - 0.151: 34 0.151 - 0.189: 5 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: 2.130 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: 0.380 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.300 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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= 0.154 Angle : 0.633 11.893 35593 Z= 0.358 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 aren 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 covalent geometry : bond 0.00305 (26281) covalent geometry : angle 0.63344 (35593) hydrogen bonds : bond 0.22460 ( 852) hydrogen bonds : angle 7.10244 ( 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 : 1.025 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: 0.1413 time to fit residues: 55.7018 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 : 0.717 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3580 r_free = 0.3580 target = 0.101203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.072367 restraints weight = 71434.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.074396 restraints weight = 40682.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.075712 restraints weight = 28314.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.076565 restraints weight = 22508.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.077091 restraints weight = 19411.820| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26281 Z= 0.222 Angle : 0.629 9.124 35593 Z= 0.325 Chirality : 0.045 0.163 3984 Planarity : 0.005 0.077 4537 Dihedral : 10.300 157.175 3679 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 2.57 % Allowed : 17.52 % Favored : 79.92 % 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 aren not related in a simple way. whole: -1.21 (0.15), residues: 3133 helix: 0.48 (0.16), residues: 1079 sheet: -1.39 (0.24), residues: 471 loop : -1.52 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 389 TYR 0.022 0.002 TYR A 482 PHE 0.016 0.002 PHE E 240 TRP 0.012 0.001 TRP D 350 HIS 0.010 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00512 (26281) covalent geometry : angle 0.62861 (35593) hydrogen bonds : bond 0.04637 ( 852) hydrogen bonds : angle 5.31468 ( 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 285 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 211 time to evaluate : 0.728 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: 0.8363 (mmm) cc_final: 0.8134 (mmm) REVERT: A 534 ASP cc_start: 0.6637 (t0) cc_final: 0.6416 (t0) REVERT: A 593 ASN cc_start: 0.8777 (m-40) cc_final: 0.8412 (t0) REVERT: A 684 MET cc_start: 0.5396 (tpt) cc_final: 0.5081 (tpt) REVERT: C 450 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8458 (mttm) REVERT: D 62 TYR cc_start: 0.6979 (m-80) cc_final: 0.6773 (m-80) REVERT: D 150 MET cc_start: 0.7948 (mmm) cc_final: 0.7605 (mmm) REVERT: D 377 LYS cc_start: 0.8696 (tptt) cc_final: 0.8335 (tptm) REVERT: D 382 GLU cc_start: 0.8437 (tp30) cc_final: 0.8130 (tp30) REVERT: D 462 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: E 223 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8277 (tp) REVERT: E 300 ASN cc_start: 0.8344 (t0) cc_final: 0.8029 (t0) REVERT: E 618 MET cc_start: 0.7801 (mtm) cc_final: 0.7407 (mtm) REVERT: K 104 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7956 (mm-30) outliers start: 74 outliers final: 43 residues processed: 266 average time/residue: 0.1252 time to fit residues: 55.8547 Evaluate side-chains 233 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 583 ILE 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 651 LEU Chi-restraints excluded: chain D residue 13 VAL 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 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: 0.6980 chunk 192 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 154 optimal weight: 0.4980 chunk 217 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.103318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.074643 restraints weight = 71519.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076714 restraints weight = 40608.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078050 restraints weight = 28281.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078909 restraints weight = 22466.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079431 restraints weight = 19409.094| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 26281 Z= 0.102 Angle : 0.524 9.451 35593 Z= 0.271 Chirality : 0.042 0.173 3984 Planarity : 0.004 0.069 4537 Dihedral : 9.808 156.165 3676 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 2.01 % Allowed : 17.66 % Favored : 80.33 % 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 aren not related in a simple way. whole: -0.94 (0.15), residues: 3133 helix: 0.73 (0.16), residues: 1068 sheet: -1.21 (0.24), residues: 479 loop : -1.38 (0.15), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 389 TYR 0.014 0.001 TYR E 82 PHE 0.017 0.001 PHE F 543 TRP 0.009 0.001 TRP C 350 HIS 0.004 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00231 (26281) covalent geometry : angle 0.52440 (35593) hydrogen bonds : bond 0.03509 ( 852) hydrogen bonds : angle 4.70109 ( 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 284 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8342 (mmm) cc_final: 0.8130 (mmm) REVERT: A 534 ASP cc_start: 0.6509 (t70) cc_final: 0.6221 (t0) REVERT: A 593 ASN cc_start: 0.8777 (m-40) cc_final: 0.8377 (t0) REVERT: A 656 ASP cc_start: 0.8898 (p0) cc_final: 0.8504 (t0) REVERT: C 450 LYS cc_start: 0.8620 (mtpt) cc_final: 0.8212 (mttp) REVERT: D 62 TYR cc_start: 0.6938 (m-80) cc_final: 0.6723 (m-80) REVERT: D 150 MET cc_start: 0.7913 (mmm) cc_final: 0.7586 (mmm) REVERT: D 322 ASP cc_start: 0.7924 (p0) cc_final: 0.7576 (p0) REVERT: D 377 LYS cc_start: 0.8665 (tptt) cc_final: 0.8217 (tptm) REVERT: D 382 GLU cc_start: 0.8411 (tp30) cc_final: 0.8181 (tp30) REVERT: D 684 MET cc_start: 0.8700 (ttp) cc_final: 0.8313 (ttp) REVERT: E 116 MET cc_start: 0.7784 (ptp) cc_final: 0.7266 (ppp) REVERT: E 223 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8240 (tp) REVERT: E 300 ASN cc_start: 0.8255 (t0) cc_final: 0.7840 (t0) REVERT: E 455 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6318 (t) REVERT: E 618 MET cc_start: 0.7831 (mtm) cc_final: 0.7405 (mtm) outliers start: 58 outliers final: 33 residues processed: 267 average time/residue: 0.1410 time to fit residues: 62.4771 Evaluate side-chains 227 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 B residue 520 ILE Chi-restraints excluded: chain B residue 536 LEU 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 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 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 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 455 SER Chi-restraints excluded: chain F residue 396 ILE 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: 9.9990 chunk 264 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 17 optimal weight: 0.4980 chunk 159 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 593 ASN E 597 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 ASN K 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.103533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.074746 restraints weight = 71138.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.076791 restraints weight = 40823.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.078159 restraints weight = 28629.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.079004 restraints weight = 22761.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079436 restraints weight = 19733.530| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.102 Angle : 0.510 8.917 35593 Z= 0.263 Chirality : 0.041 0.173 3984 Planarity : 0.004 0.065 4537 Dihedral : 9.563 156.646 3676 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.29 % Allowed : 18.04 % Favored : 79.67 % 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 aren not related in a simple way. whole: -0.77 (0.15), residues: 3133 helix: 0.90 (0.16), residues: 1064 sheet: -1.08 (0.24), residues: 469 loop : -1.31 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 665 TYR 0.013 0.001 TYR E 699 PHE 0.019 0.001 PHE F 543 TRP 0.008 0.001 TRP C 350 HIS 0.005 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00225 (26281) covalent geometry : angle 0.50970 (35593) hydrogen bonds : bond 0.03135 ( 852) hydrogen bonds : angle 4.46475 ( 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 281 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 0.956 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: 0.8410 (mmm) cc_final: 0.8188 (mmm) REVERT: A 534 ASP cc_start: 0.6530 (t70) cc_final: 0.6207 (t0) REVERT: A 593 ASN cc_start: 0.8766 (m-40) cc_final: 0.8346 (t0) REVERT: A 618 MET cc_start: 0.7183 (pmm) cc_final: 0.6935 (pmm) REVERT: A 656 ASP cc_start: 0.8863 (p0) cc_final: 0.8529 (t0) REVERT: C 340 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8572 (mm) REVERT: D 110 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8184 (tp30) REVERT: D 150 MET cc_start: 0.7956 (mmm) cc_final: 0.7491 (mmm) REVERT: D 377 LYS cc_start: 0.8553 (tptt) cc_final: 0.8140 (tptm) REVERT: D 462 MET cc_start: 0.8760 (mmm) cc_final: 0.8376 (tpt) REVERT: E 116 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7309 (ppp) REVERT: E 214 MET cc_start: 0.2997 (mtt) cc_final: 0.2710 (mtt) REVERT: E 223 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (tp) REVERT: E 290 HIS cc_start: 0.5640 (m-70) cc_final: 0.5400 (m170) REVERT: E 300 ASN cc_start: 0.8259 (t0) cc_final: 0.7815 (t0) REVERT: E 455 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.6622 (t) REVERT: E 618 MET cc_start: 0.7860 (mtm) cc_final: 0.7462 (mtm) REVERT: F 632 GLN cc_start: 0.1948 (OUTLIER) cc_final: 0.1316 (mp-120) outliers start: 66 outliers final: 43 residues processed: 259 average time/residue: 0.1331 time to fit residues: 58.5817 Evaluate side-chains 239 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 340 LEU 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 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 547 MET 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 116 MET Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL 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 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU 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 543 PHE Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 632 GLN Chi-restraints excluded: chain F residue 700 LEU 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: 1.9990 chunk 46 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 263 optimal weight: 0.3980 chunk 211 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 175 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.074402 restraints weight = 71702.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076459 restraints weight = 41340.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077812 restraints weight = 28929.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.078663 restraints weight = 23044.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.079187 restraints weight = 19969.258| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 26281 Z= 0.106 Angle : 0.513 9.517 35593 Z= 0.263 Chirality : 0.041 0.171 3984 Planarity : 0.004 0.063 4537 Dihedral : 9.332 156.532 3673 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 2.57 % Allowed : 18.42 % Favored : 79.01 % 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 aren not related in a simple way. whole: -0.70 (0.15), residues: 3133 helix: 0.96 (0.16), residues: 1072 sheet: -1.07 (0.24), residues: 464 loop : -1.27 (0.15), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 665 TYR 0.013 0.001 TYR A 482 PHE 0.018 0.001 PHE F 610 TRP 0.007 0.001 TRP C 350 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00245 (26281) covalent geometry : angle 0.51296 (35593) hydrogen bonds : bond 0.03023 ( 852) hydrogen bonds : angle 4.34761 ( 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 293 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 219 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9527 (tp) cc_final: 0.9304 (tp) REVERT: A 462 MET cc_start: 0.8435 (mmm) cc_final: 0.8221 (mmm) REVERT: A 529 GLN cc_start: 0.8139 (mp10) cc_final: 0.7933 (mp10) REVERT: A 534 ASP cc_start: 0.6583 (t70) cc_final: 0.6237 (t0) REVERT: A 593 ASN cc_start: 0.8759 (m-40) cc_final: 0.8254 (t0) REVERT: A 618 MET cc_start: 0.7212 (pmm) cc_final: 0.6931 (pmm) REVERT: A 656 ASP cc_start: 0.8823 (p0) cc_final: 0.8543 (t0) REVERT: C 340 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8573 (mm) REVERT: C 450 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8295 (mttp) REVERT: D 110 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8225 (tp30) REVERT: D 150 MET cc_start: 0.7961 (mmm) cc_final: 0.7586 (mmm) REVERT: D 382 GLU cc_start: 0.8377 (tp30) cc_final: 0.8173 (tp30) REVERT: E 116 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7408 (ppp) REVERT: E 223 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8269 (tp) REVERT: E 290 HIS cc_start: 0.5611 (m-70) cc_final: 0.5376 (m170) REVERT: E 300 ASN cc_start: 0.8225 (t0) cc_final: 0.7756 (t0) REVERT: E 455 SER cc_start: 0.7614 (OUTLIER) cc_final: 0.7168 (t) REVERT: E 618 MET cc_start: 0.7889 (mtm) cc_final: 0.7462 (mtm) REVERT: F 632 GLN cc_start: 0.1967 (OUTLIER) cc_final: 0.1334 (mp-120) REVERT: K 104 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7783 (mm-30) REVERT: K 116 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7453 (mtm) outliers start: 74 outliers final: 48 residues processed: 274 average time/residue: 0.1551 time to fit residues: 71.7954 Evaluate side-chains 252 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 632 GLN 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 340 LEU 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 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 659 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 116 MET 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 455 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 474 GLU 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 449 THR 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 116 MET Chi-restraints excluded: chain K residue 135 ILE 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: 0.9990 chunk 303 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 62 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.103687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.075080 restraints weight = 71358.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.077164 restraints weight = 40649.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078551 restraints weight = 28349.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079407 restraints weight = 22426.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.079922 restraints weight = 19382.697| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.096 Angle : 0.520 12.060 35593 Z= 0.263 Chirality : 0.041 0.189 3984 Planarity : 0.003 0.059 4537 Dihedral : 9.135 156.319 3673 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.60 % Allowed : 18.52 % Favored : 78.88 % 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 aren not related in a simple way. whole: -0.64 (0.15), residues: 3133 helix: 0.97 (0.16), residues: 1085 sheet: -1.00 (0.24), residues: 479 loop : -1.23 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 249 TYR 0.021 0.001 TYR K 82 PHE 0.014 0.001 PHE D 68 TRP 0.008 0.001 TRP C 350 HIS 0.010 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00217 (26281) covalent geometry : angle 0.52004 (35593) hydrogen bonds : bond 0.02827 ( 852) hydrogen bonds : angle 4.18694 ( 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 302 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 227 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9534 (tp) cc_final: 0.9306 (tp) REVERT: A 462 MET cc_start: 0.8458 (mmm) cc_final: 0.8254 (mmm) REVERT: A 529 GLN cc_start: 0.8248 (mp10) cc_final: 0.7879 (mp10) REVERT: A 534 ASP cc_start: 0.6575 (t70) cc_final: 0.6192 (t0) REVERT: A 593 ASN cc_start: 0.8762 (m-40) cc_final: 0.8224 (t0) REVERT: A 618 MET cc_start: 0.7171 (pmm) cc_final: 0.6892 (pmm) REVERT: A 656 ASP cc_start: 0.8792 (p0) cc_final: 0.8565 (t0) REVERT: C 340 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8601 (mm) REVERT: D 110 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8221 (tp30) REVERT: D 150 MET cc_start: 0.8004 (mmm) cc_final: 0.7678 (mmm) REVERT: D 462 MET cc_start: 0.8760 (mmm) cc_final: 0.8362 (tpt) REVERT: E 116 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7376 (ppp) REVERT: E 170 ASP cc_start: 0.7973 (t0) cc_final: 0.6688 (p0) REVERT: E 223 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8246 (tp) REVERT: E 455 SER cc_start: 0.7484 (OUTLIER) cc_final: 0.7061 (t) REVERT: E 618 MET cc_start: 0.7865 (mtm) cc_final: 0.7406 (mtm) REVERT: F 632 GLN cc_start: 0.1994 (OUTLIER) cc_final: 0.1351 (mp-120) REVERT: F 682 PRO cc_start: 0.7907 (Cg_endo) cc_final: 0.7648 (Cg_exo) REVERT: K 104 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7748 (mm-30) outliers start: 75 outliers final: 55 residues processed: 278 average time/residue: 0.1553 time to fit residues: 73.0027 Evaluate side-chains 263 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 203 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 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 452 VAL 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 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 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN 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 498 LEU Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 547 MET Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET 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 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 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 548 HIS 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 32 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 94 optimal weight: 0.9990 chunk 281 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 463 ASN E 328 ASN ** 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 = 0.3566 r_free = 0.3566 target = 0.100085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.071109 restraints weight = 72514.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.073203 restraints weight = 40687.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074584 restraints weight = 28252.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.075457 restraints weight = 22370.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075994 restraints weight = 19317.086| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26281 Z= 0.207 Angle : 0.616 12.168 35593 Z= 0.312 Chirality : 0.043 0.188 3984 Planarity : 0.004 0.058 4537 Dihedral : 9.345 156.748 3673 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 2.84 % Allowed : 19.39 % Favored : 77.77 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 3133 helix: 0.89 (0.16), residues: 1095 sheet: -1.11 (0.24), residues: 478 loop : -1.32 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 551 TYR 0.024 0.001 TYR A 482 PHE 0.028 0.002 PHE K 100 TRP 0.016 0.001 TRP D 350 HIS 0.011 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00480 (26281) covalent geometry : angle 0.61645 (35593) hydrogen bonds : bond 0.03748 ( 852) hydrogen bonds : angle 4.61380 ( 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 286 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 204 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8593 (mmm) cc_final: 0.8352 (mmm) REVERT: A 593 ASN cc_start: 0.8901 (m-40) cc_final: 0.8402 (t0) REVERT: A 618 MET cc_start: 0.7162 (pmm) cc_final: 0.6881 (pmm) REVERT: A 656 ASP cc_start: 0.8871 (p0) cc_final: 0.8585 (t0) REVERT: B 575 LYS cc_start: 0.8869 (tppt) cc_final: 0.8632 (tppt) REVERT: C 340 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (mt) REVERT: D 110 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8212 (tp30) REVERT: D 150 MET cc_start: 0.7782 (mmm) cc_final: 0.7480 (mmm) REVERT: D 377 LYS cc_start: 0.8653 (tptt) cc_final: 0.8405 (tptm) REVERT: E 116 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7182 (ppp) REVERT: E 170 ASP cc_start: 0.7973 (t0) cc_final: 0.6976 (p0) REVERT: E 223 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 455 SER cc_start: 0.7487 (OUTLIER) cc_final: 0.7175 (t) REVERT: E 618 MET cc_start: 0.8037 (mtm) cc_final: 0.7607 (mtm) REVERT: F 632 GLN cc_start: 0.1889 (OUTLIER) cc_final: 0.1309 (mp-120) REVERT: F 682 PRO cc_start: 0.7980 (Cg_endo) cc_final: 0.7767 (Cg_exo) outliers start: 82 outliers final: 58 residues processed: 266 average time/residue: 0.1492 time to fit residues: 68.1489 Evaluate side-chains 252 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 189 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 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 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN 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 54 GLU Chi-restraints excluded: chain D residue 55 SER 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 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 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 116 MET 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 274 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 382 GLU 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 E residue 621 ILE Chi-restraints excluded: chain F residue 363 LEU 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 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 257 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 238 optimal weight: 0.7980 chunk 284 optimal weight: 0.1980 chunk 159 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 143 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 287 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 201 HIS F 347 HIS ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.102705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.074554 restraints weight = 73269.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.076606 restraints weight = 42856.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.077925 restraints weight = 30176.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078799 restraints weight = 24144.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.079301 restraints weight = 20893.192| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26281 Z= 0.100 Angle : 0.545 11.388 35593 Z= 0.274 Chirality : 0.041 0.187 3984 Planarity : 0.003 0.056 4537 Dihedral : 9.132 155.716 3673 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.39 % Allowed : 20.01 % Favored : 77.59 % 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 aren not related in a simple way. whole: -0.61 (0.15), residues: 3133 helix: 1.00 (0.16), residues: 1093 sheet: -1.06 (0.24), residues: 498 loop : -1.20 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 152 TYR 0.017 0.001 TYR K 82 PHE 0.016 0.001 PHE F 543 TRP 0.010 0.001 TRP C 350 HIS 0.008 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00227 (26281) covalent geometry : angle 0.54540 (35593) hydrogen bonds : bond 0.02922 ( 852) hydrogen bonds : angle 4.24617 ( 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 284 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 215 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9538 (tp) cc_final: 0.9326 (tp) REVERT: A 593 ASN cc_start: 0.8842 (m-40) cc_final: 0.8310 (t0) REVERT: A 618 MET cc_start: 0.7185 (pmm) cc_final: 0.6891 (pmm) REVERT: B 615 ASN cc_start: 0.8696 (t0) cc_final: 0.8461 (t0) REVERT: B 618 MET cc_start: 0.7184 (mtm) cc_final: 0.6922 (mtm) REVERT: C 340 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8643 (mm) REVERT: D 110 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8237 (tp30) REVERT: D 116 MET cc_start: 0.7824 (ttp) cc_final: 0.7356 (ppp) REVERT: D 150 MET cc_start: 0.7700 (mmm) cc_final: 0.7444 (mmm) REVERT: D 377 LYS cc_start: 0.8554 (tptt) cc_final: 0.8250 (tptm) REVERT: D 462 MET cc_start: 0.8753 (mmm) cc_final: 0.8369 (tpt) REVERT: E 116 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.7314 (ppp) REVERT: E 170 ASP cc_start: 0.7918 (t0) cc_final: 0.6987 (p0) REVERT: E 223 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8213 (tp) REVERT: E 618 MET cc_start: 0.7907 (mtm) cc_final: 0.7505 (mtm) REVERT: F 632 GLN cc_start: 0.1871 (OUTLIER) cc_final: 0.1238 (mp-120) REVERT: F 682 PRO cc_start: 0.7947 (Cg_endo) cc_final: 0.7725 (Cg_exo) REVERT: K 1 MET cc_start: 0.2807 (tpp) cc_final: 0.2393 (tpp) outliers start: 69 outliers final: 51 residues processed: 267 average time/residue: 0.1525 time to fit residues: 69.0585 Evaluate side-chains 252 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 197 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 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 340 LEU 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 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 505 THR Chi-restraints excluded: chain D residue 544 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 116 MET 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 F residue 363 LEU Chi-restraints excluded: chain F residue 377 LYS 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 135 ILE 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: 0.0980 chunk 259 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 268 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 200 optimal weight: 20.0000 chunk 190 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** 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 = 0.3600 r_free = 0.3600 target = 0.101888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073807 restraints weight = 73085.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.075835 restraints weight = 42793.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077147 restraints weight = 30236.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.077991 restraints weight = 24192.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.078543 restraints weight = 20944.876| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26281 Z= 0.121 Angle : 0.560 10.800 35593 Z= 0.281 Chirality : 0.042 0.237 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.080 156.386 3671 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.29 % Allowed : 20.57 % Favored : 77.14 % 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 aren not related in a simple way. whole: -0.57 (0.15), residues: 3133 helix: 1.05 (0.16), residues: 1093 sheet: -1.06 (0.24), residues: 498 loop : -1.18 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 152 TYR 0.018 0.001 TYR K 82 PHE 0.017 0.001 PHE F 543 TRP 0.008 0.001 TRP D 350 HIS 0.009 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00282 (26281) covalent geometry : angle 0.56017 (35593) hydrogen bonds : bond 0.03038 ( 852) hydrogen bonds : angle 4.25744 ( 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 272 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 206 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9543 (tp) cc_final: 0.9334 (tp) REVERT: A 534 ASP cc_start: 0.7291 (t70) cc_final: 0.6838 (t0) REVERT: A 593 ASN cc_start: 0.8844 (m-40) cc_final: 0.8333 (t0) REVERT: C 340 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8645 (mm) REVERT: D 110 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8214 (tp30) REVERT: D 116 MET cc_start: 0.7919 (ttp) cc_final: 0.7407 (ppp) REVERT: D 150 MET cc_start: 0.7644 (mmm) cc_final: 0.7426 (mmm) REVERT: D 377 LYS cc_start: 0.8554 (tptt) cc_final: 0.8337 (tptm) REVERT: D 462 MET cc_start: 0.8764 (mmm) cc_final: 0.8371 (tpt) REVERT: E 116 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7295 (ppp) REVERT: E 170 ASP cc_start: 0.7916 (t0) cc_final: 0.7067 (p0) REVERT: E 214 MET cc_start: 0.3809 (mtm) cc_final: 0.3372 (tpt) REVERT: E 223 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (tp) REVERT: E 618 MET cc_start: 0.7930 (mtm) cc_final: 0.7483 (mtm) REVERT: F 632 GLN cc_start: 0.1916 (OUTLIER) cc_final: 0.1255 (mp-120) REVERT: F 682 PRO cc_start: 0.7878 (Cg_endo) cc_final: 0.7667 (Cg_exo) REVERT: K 1 MET cc_start: 0.2788 (tpp) cc_final: 0.2374 (tpp) outliers start: 66 outliers final: 54 residues processed: 255 average time/residue: 0.1640 time to fit residues: 71.0627 Evaluate side-chains 258 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 200 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 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 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 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN 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 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 505 THR Chi-restraints excluded: chain D residue 544 ILE 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 116 MET 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 669 LEU Chi-restraints excluded: chain F residue 363 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 128 optimal weight: 0.4980 chunk 193 optimal weight: 7.9990 chunk 145 optimal weight: 0.3980 chunk 135 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 274 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.073438 restraints weight = 73206.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.075447 restraints weight = 43063.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.076774 restraints weight = 30499.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.077615 restraints weight = 24391.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.078043 restraints weight = 21188.568| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.128 Angle : 0.571 13.130 35593 Z= 0.286 Chirality : 0.042 0.195 3984 Planarity : 0.004 0.059 4537 Dihedral : 9.069 156.087 3671 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.32 % Allowed : 20.71 % Favored : 76.97 % 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 aren not related in a simple way. whole: -0.54 (0.15), residues: 3133 helix: 1.06 (0.16), residues: 1097 sheet: -1.03 (0.24), residues: 479 loop : -1.16 (0.15), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 152 TYR 0.018 0.001 TYR K 82 PHE 0.017 0.001 PHE F 543 TRP 0.009 0.001 TRP C 350 HIS 0.009 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00300 (26281) covalent geometry : angle 0.57068 (35593) hydrogen bonds : bond 0.03075 ( 852) hydrogen bonds : angle 4.26897 ( 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 271 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 ILE cc_start: 0.9547 (tp) cc_final: 0.9339 (tp) REVERT: A 534 ASP cc_start: 0.7398 (t70) cc_final: 0.7085 (t0) REVERT: A 593 ASN cc_start: 0.8870 (m-40) cc_final: 0.8397 (t0) REVERT: A 617 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7533 (tt) REVERT: B 615 ASN cc_start: 0.8591 (t0) cc_final: 0.8286 (p0) REVERT: C 340 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8664 (mm) REVERT: C 447 ASP cc_start: 0.7259 (t0) cc_final: 0.7031 (t0) REVERT: C 450 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8339 (mttp) REVERT: C 557 GLU cc_start: 0.6452 (pm20) cc_final: 0.6140 (pm20) REVERT: D 116 MET cc_start: 0.7888 (ttp) cc_final: 0.7385 (ppp) REVERT: D 150 MET cc_start: 0.7570 (mmm) cc_final: 0.7226 (mmm) REVERT: D 377 LYS cc_start: 0.8538 (tptt) cc_final: 0.8330 (tptm) REVERT: D 462 MET cc_start: 0.8782 (mmm) cc_final: 0.8354 (tpt) REVERT: E 116 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7285 (ppp) REVERT: E 170 ASP cc_start: 0.7801 (t0) cc_final: 0.7182 (p0) REVERT: E 214 MET cc_start: 0.4213 (mtm) cc_final: 0.3533 (tpt) REVERT: E 618 MET cc_start: 0.7956 (mtm) cc_final: 0.7553 (mtm) REVERT: F 632 GLN cc_start: 0.1898 (OUTLIER) cc_final: 0.1268 (mp-120) REVERT: K 1 MET cc_start: 0.2749 (tpp) cc_final: 0.2314 (tpp) outliers start: 67 outliers final: 58 residues processed: 253 average time/residue: 0.1521 time to fit residues: 65.7436 Evaluate side-chains 257 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 195 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 617 LEU 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 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 340 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN 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 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 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 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET 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 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 548 HIS 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 K residue 32 VAL Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 160 optimal weight: 0.0020 chunk 200 optimal weight: 3.9990 chunk 295 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 280 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** 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 = 0.3585 r_free = 0.3585 target = 0.101088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.072996 restraints weight = 73008.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.075017 restraints weight = 43110.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.076312 restraints weight = 30568.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.077124 restraints weight = 24521.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.077659 restraints weight = 21321.819| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.139 Angle : 0.576 12.661 35593 Z= 0.290 Chirality : 0.042 0.186 3984 Planarity : 0.004 0.062 4537 Dihedral : 9.071 156.127 3671 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.40 % Rotamer: Outliers : 2.25 % Allowed : 20.95 % Favored : 76.80 % 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 aren not related in a simple way. whole: -0.56 (0.15), residues: 3133 helix: 1.04 (0.16), residues: 1102 sheet: -0.99 (0.25), residues: 469 loop : -1.19 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 152 TYR 0.018 0.001 TYR K 82 PHE 0.017 0.001 PHE D 35 TRP 0.010 0.001 TRP D 350 HIS 0.007 0.001 HIS F 548 Details of bonding type rmsd covalent geometry : bond 0.00326 (26281) covalent geometry : angle 0.57616 (35593) hydrogen bonds : bond 0.03103 ( 852) hydrogen bonds : angle 4.29092 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.75 seconds wall clock time: 70 minutes 18.85 seconds (4218.85 seconds total)