Starting phenix.real_space_refine on Fri Feb 6 14:32:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.cif Found real_map, /net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9im2_60680/02_2026/9im2_60680.map" } resolution = 3.12 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= 0.021 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 19 5.49 5 Mg 3 5.21 5 S 121 5.16 5 C 16445 2.51 5 N 4341 2.21 5 O 4880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25809 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4414 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 519} Chain: "F" Number of atoms: 3575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3575 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3764 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain: "B" Number of atoms: 3764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3764 Classifications: {'peptide': 465} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain: "C" Number of atoms: 5592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5592 Classifications: {'peptide': 690} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 661} Chain breaks: 1 Chain: "D" Number of atoms: 4414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4414 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 519} Chain: "X" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna3p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna3p': 1} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.69, per 1000 atoms: 0.22 Number of scatterers: 25809 At special positions: 0 Unit cell: (139.92, 137.28, 162.8, 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 121 16.00 P 19 15.00 Mg 3 11.99 O 4880 8.00 N 4341 7.00 C 16445 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 285 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 808.3 milliseconds 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6040 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 46 sheets defined 45.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'E' and resid 244 through 254 removed outlier: 3.589A pdb=" N LYS E 248 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE E 254 " --> pdb=" O VAL E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.668A pdb=" N ASN E 262 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP E 263 " --> pdb=" O ASN E 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 259 through 263' Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 324 through 336 removed outlier: 3.811A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 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: 3.516A pdb=" N SER E 380 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 376 through 381' 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 399 Processing helix chain 'E' and resid 430 through 436 removed outlier: 4.076A pdb=" N TYR E 436 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 removed outlier: 3.553A pdb=" N GLU E 459 " --> pdb=" O SER E 455 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 510 through 521 removed outlier: 3.567A pdb=" N ARG E 514 " --> pdb=" O SER E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 533 removed outlier: 3.731A pdb=" N ILE E 531 " --> pdb=" O GLY E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 548 removed outlier: 3.587A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS E 548 " --> pdb=" O ILE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 579 removed outlier: 4.053A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 578 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU E 579 " --> pdb=" O LYS E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 Processing helix chain 'E' and resid 653 through 661 removed outlier: 3.993A pdb=" N GLY E 657 " --> pdb=" O GLU E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 Processing helix chain 'E' and resid 693 through 705 Processing helix chain 'E' and resid 710 through 714 Processing helix chain 'E' and resid 716 through 723 removed outlier: 3.578A pdb=" N LYS E 722 " --> pdb=" O THR E 718 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 723 " --> pdb=" O ASP E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 747 removed outlier: 3.799A pdb=" N TYR E 746 " --> pdb=" O LYS E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 764 removed outlier: 6.956A pdb=" N HIS E 754 " --> pdb=" O ARG E 750 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASP E 755 " --> pdb=" O LEU E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 779 through 783 Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 362 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 384 removed outlier: 3.808A pdb=" N SER F 380 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 456 through 469 removed outlier: 3.675A pdb=" N ASN F 463 " --> pdb=" O GLU F 459 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 491 removed outlier: 3.766A pdb=" N LEU F 490 " --> pdb=" O LEU F 486 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS F 491 " --> pdb=" O SER F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 529 through 534 removed outlier: 3.711A pdb=" N THR F 533 " --> pdb=" O GLN F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 547 removed outlier: 3.679A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 578 removed outlier: 3.510A 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 655 through 661 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 696 through 705 Processing helix chain 'F' and resid 710 through 714 Processing helix chain 'F' and resid 716 through 721 Processing helix chain 'F' and resid 722 through 724 No H-bonds generated for 'chain 'F' and resid 722 through 724' Processing helix chain 'F' and resid 735 through 747 removed outlier: 3.893A pdb=" N TYR F 746 " --> pdb=" O LYS F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 752 through 763 Processing helix chain 'F' and resid 779 through 783 Processing helix chain 'A' and resid 324 through 336 removed outlier: 3.663A pdb=" N THR A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 371 Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 385 through 400 removed outlier: 3.503A pdb=" N LEU A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 475 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 528 through 533 removed outlier: 4.052A 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: 3.539A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.515A pdb=" N ASN A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 680 Processing helix chain 'A' and resid 693 through 705 removed outlier: 3.900A pdb=" N PHE A 698 " --> pdb=" O PRO A 694 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 699 " --> pdb=" O ASP A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 714 removed outlier: 3.585A pdb=" N ILE A 714 " --> pdb=" O VAL A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 724 Processing helix chain 'A' and resid 736 through 747 Processing helix chain 'A' and resid 752 through 763 removed outlier: 3.597A pdb=" N HIS A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 783 Processing helix chain 'B' and resid 324 through 336 removed outlier: 3.774A pdb=" N THR B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 376 through 385 removed outlier: 3.945A pdb=" N SER B 380 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N CYS B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 430 through 435 removed outlier: 3.804A pdb=" N LYS B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 472 through 489 removed outlier: 4.569A pdb=" N LYS B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ASN B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 486 " --> pdb=" O TYR B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.514A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.733A pdb=" N GLU B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 661 removed outlier: 3.643A pdb=" N LYS B 658 " --> pdb=" O GLY B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 Processing helix chain 'B' and resid 693 through 705 Processing helix chain 'B' and resid 710 through 715 Proline residue: B 715 - end of helix Processing helix chain 'B' and resid 716 through 721 removed outlier: 3.580A pdb=" N LEU B 720 " --> pdb=" O LEU B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 735 through 744 Processing helix chain 'B' and resid 748 through 763 removed outlier: 6.556A pdb=" N HIS B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP B 755 " --> pdb=" O LEU B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 783 Processing helix chain 'C' and resid 20 through 26 Processing helix chain 'C' and resid 36 through 47 Processing helix chain 'C' and resid 78 through 104 Processing helix chain 'C' and resid 108 through 119 removed outlier: 4.006A pdb=" N ASN C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.402A pdb=" N ARG C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 3.733A pdb=" N ILE C 169 " --> pdb=" O THR C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 174 removed outlier: 4.093A pdb=" N VAL C 173 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.936A pdb=" N LEU C 208 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 removed outlier: 3.801A pdb=" N THR C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 372 removed outlier: 3.593A pdb=" N LYS C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 Processing helix chain 'C' and resid 382 through 384 No H-bonds generated for 'chain 'C' and resid 382 through 384' Processing helix chain 'C' and resid 385 through 400 Processing helix chain 'C' and resid 430 through 435 removed outlier: 3.797A pdb=" N LYS C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'C' and resid 528 through 533 removed outlier: 4.003A 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 578 removed outlier: 3.619A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.539A 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 640 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 693 through 705 removed outlier: 3.689A pdb=" N ALA C 697 " --> pdb=" O ILE C 693 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE C 698 " --> pdb=" O PRO C 694 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 710 through 715 Proline residue: C 715 - end of helix Processing helix chain 'C' and resid 716 through 721 Processing helix chain 'C' and resid 722 through 724 No H-bonds generated for 'chain 'C' and resid 722 through 724' Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.537A pdb=" N LYS C 745 " --> pdb=" O GLN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 6.329A pdb=" N HIS C 754 " --> pdb=" O ARG C 750 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP C 755 " --> pdb=" O LEU C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 783 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 310 through 314 removed outlier: 3.678A pdb=" N CYS D 314 " --> pdb=" O PRO D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.734A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.655A pdb=" N LYS D 366 " --> pdb=" O PRO D 362 " (cutoff:3.500A) 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 385 removed outlier: 3.896A pdb=" N SER D 380 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N CYS D 385 " --> pdb=" O SER D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 399 Processing helix chain 'D' and resid 429 through 436 Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 541 through 548 removed outlier: 3.514A pdb=" N HIS D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 577 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.771A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 634 No H-bonds generated for 'chain 'D' and resid 632 through 634' Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 656 through 661 Processing helix chain 'D' and resid 664 through 680 removed outlier: 3.572A pdb=" N LEU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 671 " --> pdb=" O ALA D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 705 removed outlier: 3.804A pdb=" N ALA D 697 " --> pdb=" O ILE D 693 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE D 698 " --> pdb=" O PRO D 694 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY D 703 " --> pdb=" O TYR D 699 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 704 " --> pdb=" O LEU D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 715 Proline residue: D 715 - end of helix Processing helix chain 'D' and resid 716 through 724 Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.971A pdb=" N LYS D 745 " --> pdb=" O GLN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 751 No H-bonds generated for 'chain 'D' and resid 749 through 751' Processing helix chain 'D' and resid 752 through 763 Processing sheet with id=AA1, first strand: chain 'E' and resid 294 through 299 Processing sheet with id=AA2, first strand: chain 'E' and resid 339 through 341 Processing sheet with id=AA3, first strand: chain 'E' and resid 412 through 414 Processing sheet with id=AA4, first strand: chain 'E' and resid 524 through 526 removed outlier: 6.685A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 581 through 583 Processing sheet with id=AA6, first strand: chain 'E' and resid 629 through 630 removed outlier: 7.433A pdb=" N HIS E 629 " --> pdb=" O LYS E 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 706 through 708 Processing sheet with id=AA8, first strand: chain 'E' and resid 726 through 728 Processing sheet with id=AA9, first strand: chain 'E' and resid 765 through 766 Processing sheet with id=AB1, first strand: chain 'F' and resid 339 through 341 Processing sheet with id=AB2, first strand: chain 'F' and resid 412 through 414 Processing sheet with id=AB3, first strand: chain 'F' and resid 524 through 526 removed outlier: 6.850A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY F 503 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 706 through 707 Processing sheet with id=AB5, first strand: chain 'F' and resid 726 through 728 Processing sheet with id=AB6, first strand: chain 'F' and resid 765 through 766 Processing sheet with id=AB7, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AB8, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.843A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.848A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 503 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AC2, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.821A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 706 through 708 removed outlier: 3.798A pdb=" N VAL A 707 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 726 through 728 removed outlier: 4.206A pdb=" N LEU A 734 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 774 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 339 through 341 Processing sheet with id=AC6, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.928A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.803A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N SER B 556 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 503 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC9, first strand: chain 'B' and resid 629 through 631 removed outlier: 6.708A pdb=" N HIS B 629 " --> pdb=" O LYS B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 706 through 708 Processing sheet with id=AD2, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AD3, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AD4, first strand: chain 'C' and resid 65 through 73 removed outlier: 10.524A pdb=" N VAL C 65 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP C 139 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE C 67 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N TYR C 219 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP C 139 " --> pdb=" O TYR C 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 124 through 125 removed outlier: 3.746A pdb=" N LYS C 124 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 339 through 341 Processing sheet with id=AD7, first strand: chain 'C' and resid 412 through 414 Processing sheet with id=AD8, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.850A pdb=" N VAL C 525 " --> pdb=" O PHE C 554 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N SER C 556 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AE1, first strand: chain 'C' and resid 628 through 631 Processing sheet with id=AE2, first strand: chain 'C' and resid 706 through 708 Processing sheet with id=AE3, first strand: chain 'C' and resid 726 through 728 Processing sheet with id=AE4, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.554A pdb=" N LYS D 317 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 339 through 341 Processing sheet with id=AE6, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.913A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 524 through 527 removed outlier: 3.856A pdb=" N GLY D 503 " --> pdb=" O THR D 604 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 581 through 582 Processing sheet with id=AE9, first strand: chain 'D' and resid 629 through 631 removed outlier: 6.573A pdb=" N HIS D 629 " --> pdb=" O LYS D 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 706 through 707 950 hydrogen bonds defined for protein. 2664 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: 5.24 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8147 1.34 - 1.46: 4493 1.46 - 1.58: 13530 1.58 - 1.70: 30 1.70 - 1.82: 175 Bond restraints: 26375 Sorted by residual: bond pdb=" C ILE D 714 " pdb=" N PRO D 715 " ideal model delta sigma weight residual 1.336 1.356 -0.020 1.08e-02 8.57e+03 3.41e+00 bond pdb=" CB LYS B 538 " pdb=" CG LYS B 538 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.15e+00 bond pdb=" C ILE C 681 " pdb=" N PRO C 682 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.88e+00 bond pdb=" CB LYS A 567 " pdb=" CG LYS A 567 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" CB GLN C 632 " pdb=" CG GLN C 632 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.67e+00 ... (remaining 26370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 35343 2.23 - 4.47: 290 4.47 - 6.70: 54 6.70 - 8.93: 13 8.93 - 11.17: 6 Bond angle restraints: 35706 Sorted by residual: angle pdb=" CB LYS A 567 " pdb=" CG LYS A 567 " pdb=" CD LYS A 567 " ideal model delta sigma weight residual 111.30 120.96 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CB LYS B 538 " pdb=" CG LYS B 538 " pdb=" CD LYS B 538 " ideal model delta sigma weight residual 111.30 120.89 -9.59 2.30e+00 1.89e-01 1.74e+01 angle pdb=" C LEU E 461 " pdb=" N MET E 462 " pdb=" CA MET E 462 " ideal model delta sigma weight residual 121.14 114.42 6.72 1.75e+00 3.27e-01 1.48e+01 angle pdb=" CB MET E 547 " pdb=" CG MET E 547 " pdb=" SD MET E 547 " ideal model delta sigma weight residual 112.70 123.87 -11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CB MET F 426 " pdb=" CG MET F 426 " pdb=" SD MET F 426 " ideal model delta sigma weight residual 112.70 123.11 -10.41 3.00e+00 1.11e-01 1.21e+01 ... (remaining 35701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 15587 33.46 - 66.92: 471 66.92 - 100.37: 30 100.37 - 133.83: 1 133.83 - 167.29: 2 Dihedral angle restraints: 16091 sinusoidal: 6786 harmonic: 9305 Sorted by residual: dihedral pdb=" CB CYS E 282 " pdb=" SG CYS E 282 " pdb=" SG CYS E 285 " pdb=" CB CYS E 285 " ideal model delta sinusoidal sigma weight residual -86.00 -152.05 66.05 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" O2A ADP D 801 " pdb=" O3A ADP D 801 " pdb=" PA ADP D 801 " pdb=" PB ADP D 801 " ideal model delta sinusoidal sigma weight residual -60.00 107.29 -167.29 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' AMP E 801 " pdb=" O5' AMP E 801 " pdb=" P AMP E 801 " pdb=" O3P AMP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 84.75 -144.74 1 2.00e+01 2.50e-03 4.36e+01 ... (remaining 16088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3138 0.046 - 0.092: 662 0.092 - 0.138: 199 0.138 - 0.185: 2 0.185 - 0.231: 4 Chirality restraints: 4005 Sorted by residual: chirality pdb=" C2' AMP E 801 " pdb=" C1' AMP E 801 " pdb=" C3' AMP E 801 " pdb=" O2' AMP E 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU C 736 " pdb=" CB LEU C 736 " pdb=" CD1 LEU C 736 " pdb=" CD2 LEU C 736 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ILE A 602 " pdb=" N ILE A 602 " pdb=" C ILE A 602 " pdb=" CB ILE A 602 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 4002 not shown) Planarity restraints: 4517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 199 " 0.038 5.00e-02 4.00e+02 5.79e-02 5.37e+00 pdb=" N PRO C 200 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 200 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 200 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 693 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO F 694 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO F 694 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 694 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 455 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO F 456 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO F 456 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 456 " 0.028 5.00e-02 4.00e+02 ... (remaining 4514 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 189 2.53 - 3.12: 19679 3.12 - 3.72: 40306 3.72 - 4.31: 54076 4.31 - 4.90: 89432 Nonbonded interactions: 203682 Sorted by model distance: nonbonded pdb=" O2B ATP C 801 " pdb="MG MG C 802 " model vdw 1.940 2.170 nonbonded pdb=" O3B ATP B 801 " pdb="MG MG B 802 " model vdw 1.949 2.170 nonbonded pdb=" O3B ATP A 801 " pdb="MG MG A 802 " model vdw 1.957 2.170 nonbonded pdb=" O3B ATP C 801 " pdb="MG MG C 802 " model vdw 1.998 2.170 nonbonded pdb=" O3G ATP C 801 " pdb="MG MG C 802 " model vdw 2.009 2.170 ... (remaining 203677 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 321 through 629 or resid 654 through 785)) selection = (chain 'B' and (resid 321 through 629 or resid 654 through 785)) selection = (chain 'D' and (resid 321 through 629 or resid 654 through 785)) selection = (chain 'E' and (resid 321 through 629 or resid 654 through 785)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.270 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 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 : 0.002 0.044 26376 Z= 0.109 Angle : 0.545 11.167 35708 Z= 0.276 Chirality : 0.041 0.231 4005 Planarity : 0.003 0.058 4517 Dihedral : 15.047 167.290 10048 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.07 % Allowed : 21.63 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3137 helix: 1.33 (0.16), residues: 1187 sheet: -0.03 (0.27), residues: 423 loop : 0.06 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 514 TYR 0.021 0.001 TYR F 676 PHE 0.017 0.001 PHE A 759 TRP 0.006 0.001 TRP A 350 HIS 0.006 0.001 HIS F 680 Details of bonding type rmsd covalent geometry : bond 0.00243 (26375) covalent geometry : angle 0.54534 (35706) SS BOND : bond 0.00302 ( 1) SS BOND : angle 1.47536 ( 2) hydrogen bonds : bond 0.16235 ( 950) hydrogen bonds : angle 5.43616 ( 2664) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 262 ASN cc_start: 0.9345 (m-40) cc_final: 0.9131 (p0) REVERT: B 713 HIS cc_start: 0.7706 (m90) cc_final: 0.7450 (m90) REVERT: B 747 PHE cc_start: 0.6952 (t80) cc_final: 0.6663 (t80) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.1703 time to fit residues: 35.7900 Evaluate side-chains 125 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain D residue 740 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0010 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 605 ASN ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 ASN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 768 ASN D 337 ASN ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 775 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.102622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.063582 restraints weight = 91437.217| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.12 r_work: 0.2885 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 26376 Z= 0.235 Angle : 0.596 8.125 35708 Z= 0.308 Chirality : 0.043 0.172 4005 Planarity : 0.004 0.061 4517 Dihedral : 9.001 167.240 3621 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.07 % Allowed : 19.74 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3137 helix: 1.10 (0.15), residues: 1252 sheet: -0.06 (0.27), residues: 418 loop : -0.09 (0.17), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 514 TYR 0.024 0.001 TYR C 482 PHE 0.018 0.001 PHE D 668 TRP 0.009 0.001 TRP C 350 HIS 0.005 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00550 (26375) covalent geometry : angle 0.59587 (35706) SS BOND : bond 0.00215 ( 1) SS BOND : angle 1.58276 ( 2) hydrogen bonds : bond 0.04537 ( 950) hydrogen bonds : angle 4.63269 ( 2664) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 139 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 262 ASN cc_start: 0.9410 (m-40) cc_final: 0.9181 (p0) REVERT: E 458 MET cc_start: 0.8971 (ppp) cc_final: 0.8447 (ppp) REVERT: B 681 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8976 (mm) REVERT: B 747 PHE cc_start: 0.7027 (t80) cc_final: 0.6475 (t80) REVERT: B 766 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: C 197 MET cc_start: 0.7786 (tpp) cc_final: 0.7281 (tpp) REVERT: D 462 MET cc_start: 0.9266 (mmm) cc_final: 0.8785 (mmm) outliers start: 60 outliers final: 26 residues processed: 188 average time/residue: 0.1794 time to fit residues: 52.7898 Evaluate side-chains 150 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 734 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 741 GLN Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 766 PHE Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 739 PHE Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 48 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 206 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 219 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 GLN A 741 GLN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 605 ASN ** D 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.103235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064396 restraints weight = 92048.014| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.07 r_work: 0.2892 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26376 Z= 0.191 Angle : 0.562 11.727 35708 Z= 0.290 Chirality : 0.042 0.236 4005 Planarity : 0.004 0.062 4517 Dihedral : 8.824 173.752 3618 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.58 % Allowed : 18.95 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3137 helix: 1.08 (0.15), residues: 1249 sheet: -0.17 (0.27), residues: 410 loop : -0.13 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 551 TYR 0.019 0.001 TYR C 482 PHE 0.016 0.001 PHE A 778 TRP 0.006 0.001 TRP C 350 HIS 0.006 0.001 HIS E 763 Details of bonding type rmsd covalent geometry : bond 0.00448 (26375) covalent geometry : angle 0.56181 (35706) SS BOND : bond 0.00193 ( 1) SS BOND : angle 1.30347 ( 2) hydrogen bonds : bond 0.03980 ( 950) hydrogen bonds : angle 4.50032 ( 2664) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8942 (ppp) cc_final: 0.8730 (ppp) REVERT: F 364 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 372 ARG cc_start: 0.9597 (OUTLIER) cc_final: 0.9102 (ptp90) REVERT: B 649 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8971 (mmmm) REVERT: B 747 PHE cc_start: 0.7030 (t80) cc_final: 0.6451 (t80) REVERT: C 197 MET cc_start: 0.7802 (tpp) cc_final: 0.7262 (tpp) REVERT: D 377 LYS cc_start: 0.9218 (pmtt) cc_final: 0.8981 (pttt) REVERT: D 577 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9335 (mp) REVERT: D 717 MET cc_start: 0.8652 (mmm) cc_final: 0.8378 (mmm) outliers start: 75 outliers final: 33 residues processed: 202 average time/residue: 0.1819 time to fit residues: 57.4855 Evaluate side-chains 161 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 450 LYS Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 734 LEU Chi-restraints excluded: chain F residue 364 ILE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 618 MET Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 436 TYR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 662 ASN Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 294 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 96 optimal weight: 6.9990 chunk 218 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 192 optimal weight: 20.0000 chunk 42 optimal weight: 0.5980 chunk 298 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 775 GLN B 629 HIS ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.103919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.065396 restraints weight = 89651.007| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.10 r_work: 0.2931 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26376 Z= 0.105 Angle : 0.521 10.908 35708 Z= 0.265 Chirality : 0.041 0.172 4005 Planarity : 0.003 0.061 4517 Dihedral : 8.652 179.745 3615 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.31 % Allowed : 18.95 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 3137 helix: 1.23 (0.15), residues: 1249 sheet: -0.13 (0.27), residues: 419 loop : -0.02 (0.17), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.014 0.001 TYR A 482 PHE 0.026 0.001 PHE A 759 TRP 0.006 0.001 TRP C 350 HIS 0.005 0.001 HIS E 763 Details of bonding type rmsd covalent geometry : bond 0.00243 (26375) covalent geometry : angle 0.52047 (35706) SS BOND : bond 0.00290 ( 1) SS BOND : angle 1.14720 ( 2) hydrogen bonds : bond 0.03001 ( 950) hydrogen bonds : angle 4.22524 ( 2664) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 462 MET cc_start: 0.9137 (pmm) cc_final: 0.8923 (pmm) REVERT: F 686 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7149 (pp) REVERT: A 372 ARG cc_start: 0.9572 (OUTLIER) cc_final: 0.9029 (ptp90) REVERT: A 618 MET cc_start: 0.8946 (ptp) cc_final: 0.8733 (mtm) REVERT: B 649 LYS cc_start: 0.9349 (OUTLIER) cc_final: 0.8977 (mmmm) REVERT: B 747 PHE cc_start: 0.7023 (t80) cc_final: 0.6411 (t80) REVERT: C 197 MET cc_start: 0.7759 (tpp) cc_final: 0.7198 (tpp) REVERT: C 211 TYR cc_start: 0.7688 (t80) cc_final: 0.7363 (t80) REVERT: C 505 THR cc_start: 0.9336 (OUTLIER) cc_final: 0.9091 (t) REVERT: D 377 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (pptt) REVERT: D 717 MET cc_start: 0.8766 (mmm) cc_final: 0.8404 (mmm) REVERT: D 776 TYR cc_start: 0.8870 (m-80) cc_final: 0.8604 (m-80) outliers start: 67 outliers final: 32 residues processed: 197 average time/residue: 0.1881 time to fit residues: 57.3238 Evaluate side-chains 165 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 88 optimal weight: 2.9990 chunk 309 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 164 optimal weight: 0.9980 chunk 282 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 278 optimal weight: 0.0670 chunk 232 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 HIS D 260 ASN ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.103574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.064252 restraints weight = 90049.552| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 4.27 r_work: 0.2875 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26376 Z= 0.140 Angle : 0.531 10.006 35708 Z= 0.271 Chirality : 0.041 0.193 4005 Planarity : 0.003 0.061 4517 Dihedral : 8.551 173.047 3615 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.96 % Allowed : 18.64 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 3137 helix: 1.22 (0.15), residues: 1256 sheet: -0.22 (0.26), residues: 441 loop : -0.02 (0.17), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 514 TYR 0.017 0.001 TYR C 482 PHE 0.019 0.001 PHE A 778 TRP 0.006 0.001 TRP C 350 HIS 0.004 0.001 HIS E 763 Details of bonding type rmsd covalent geometry : bond 0.00329 (26375) covalent geometry : angle 0.53132 (35706) SS BOND : bond 0.00254 ( 1) SS BOND : angle 1.10903 ( 2) hydrogen bonds : bond 0.03322 ( 950) hydrogen bonds : angle 4.25066 ( 2664) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 133 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8955 (ppp) cc_final: 0.8207 (ppp) REVERT: E 462 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8690 (pmm) REVERT: F 686 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7363 (pp) REVERT: A 372 ARG cc_start: 0.9584 (OUTLIER) cc_final: 0.9041 (ptp90) REVERT: A 618 MET cc_start: 0.8948 (ptp) cc_final: 0.8691 (mtm) REVERT: B 747 PHE cc_start: 0.7041 (t80) cc_final: 0.6369 (t80) REVERT: C 152 ARG cc_start: 0.9283 (ttm-80) cc_final: 0.8901 (tpt-90) REVERT: C 156 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8210 (mm-30) REVERT: C 197 MET cc_start: 0.7855 (tpp) cc_final: 0.7311 (tpp) REVERT: C 505 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9104 (t) REVERT: D 377 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8994 (pptt) REVERT: D 577 LEU cc_start: 0.9582 (OUTLIER) cc_final: 0.9352 (mp) REVERT: D 717 MET cc_start: 0.8880 (mmm) cc_final: 0.8354 (mmm) REVERT: D 776 TYR cc_start: 0.8887 (m-80) cc_final: 0.8589 (m-80) outliers start: 86 outliers final: 49 residues processed: 209 average time/residue: 0.1804 time to fit residues: 58.1396 Evaluate side-chains 181 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 734 LEU Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 445 LYS Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 292 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 268 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 253 optimal weight: 9.9990 chunk 282 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN A 713 HIS ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 763 HIS D 353 ASN D 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.103876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064766 restraints weight = 90257.797| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 4.25 r_work: 0.2892 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26376 Z= 0.108 Angle : 0.519 10.453 35708 Z= 0.263 Chirality : 0.040 0.167 4005 Planarity : 0.003 0.062 4517 Dihedral : 8.440 168.551 3615 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.51 % Allowed : 18.98 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3137 helix: 1.28 (0.15), residues: 1251 sheet: -0.16 (0.26), residues: 436 loop : 0.02 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 514 TYR 0.014 0.001 TYR C 482 PHE 0.029 0.001 PHE A 759 TRP 0.006 0.001 TRP C 350 HIS 0.003 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00251 (26375) covalent geometry : angle 0.51852 (35706) SS BOND : bond 0.00286 ( 1) SS BOND : angle 1.02203 ( 2) hydrogen bonds : bond 0.02932 ( 950) hydrogen bonds : angle 4.13119 ( 2664) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 134 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8955 (ppp) cc_final: 0.8236 (ppp) REVERT: E 462 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8706 (pmm) REVERT: F 686 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7369 (pp) REVERT: F 717 MET cc_start: -0.0443 (OUTLIER) cc_final: -0.1191 (mtp) REVERT: A 372 ARG cc_start: 0.9570 (OUTLIER) cc_final: 0.8996 (ptp90) REVERT: A 618 MET cc_start: 0.8886 (ptp) cc_final: 0.8594 (mtm) REVERT: B 649 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8967 (mmmm) REVERT: B 747 PHE cc_start: 0.7064 (t80) cc_final: 0.6391 (t80) REVERT: C 152 ARG cc_start: 0.9297 (ttm-80) cc_final: 0.8884 (tpt-90) REVERT: C 156 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8211 (mm-30) REVERT: C 197 MET cc_start: 0.7844 (tpp) cc_final: 0.7263 (tpp) REVERT: C 219 TYR cc_start: 0.7689 (t80) cc_final: 0.6870 (t80) REVERT: D 377 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8972 (pptt) REVERT: D 577 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9340 (mp) REVERT: D 717 MET cc_start: 0.9018 (mmm) cc_final: 0.8508 (mmm) REVERT: D 776 TYR cc_start: 0.8884 (m-80) cc_final: 0.8585 (m-80) outliers start: 73 outliers final: 46 residues processed: 198 average time/residue: 0.1761 time to fit residues: 54.3978 Evaluate side-chains 185 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 416 LYS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 734 LEU Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 686 LEU Chi-restraints excluded: chain F residue 717 MET Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 577 LEU Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 14 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 213 optimal weight: 0.5980 chunk 144 optimal weight: 0.3980 chunk 130 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.103431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064838 restraints weight = 90921.256| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.19 r_work: 0.2911 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26376 Z= 0.094 Angle : 0.511 9.230 35708 Z= 0.258 Chirality : 0.040 0.166 4005 Planarity : 0.003 0.062 4517 Dihedral : 8.287 166.948 3615 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.34 % Allowed : 19.08 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3137 helix: 1.32 (0.15), residues: 1251 sheet: -0.21 (0.26), residues: 426 loop : 0.07 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 514 TYR 0.013 0.001 TYR C 482 PHE 0.021 0.001 PHE A 778 TRP 0.006 0.001 TRP C 350 HIS 0.009 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00217 (26375) covalent geometry : angle 0.51139 (35706) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.96288 ( 2) hydrogen bonds : bond 0.02688 ( 950) hydrogen bonds : angle 4.02222 ( 2664) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 139 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8970 (ppp) cc_final: 0.8248 (ppp) REVERT: E 462 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8647 (pmm) REVERT: F 626 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.3983 (m-80) REVERT: F 717 MET cc_start: -0.0439 (OUTLIER) cc_final: -0.1187 (mtp) REVERT: A 372 ARG cc_start: 0.9555 (OUTLIER) cc_final: 0.9041 (ptp90) REVERT: A 618 MET cc_start: 0.8845 (ptp) cc_final: 0.8534 (mtm) REVERT: B 649 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8952 (mmmm) REVERT: B 747 PHE cc_start: 0.7088 (t80) cc_final: 0.6451 (t80) REVERT: C 152 ARG cc_start: 0.9312 (ttm-80) cc_final: 0.8884 (tpt-90) REVERT: C 156 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8285 (mm-30) REVERT: C 197 MET cc_start: 0.7806 (tpp) cc_final: 0.7179 (tpp) REVERT: C 219 TYR cc_start: 0.7735 (t80) cc_final: 0.6851 (t80) REVERT: D 377 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8932 (pptt) REVERT: D 717 MET cc_start: 0.9053 (mmm) cc_final: 0.8484 (mmm) REVERT: D 755 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8594 (p0) REVERT: D 776 TYR cc_start: 0.8865 (m-80) cc_final: 0.8535 (m-80) outliers start: 68 outliers final: 47 residues processed: 199 average time/residue: 0.1758 time to fit residues: 54.8767 Evaluate side-chains 187 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 133 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 717 MET Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 353 ASN Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 713 HIS Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 754 HIS Chi-restraints excluded: chain D residue 755 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 250 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 172 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 230 optimal weight: 0.0770 chunk 205 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.102983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064835 restraints weight = 92896.417| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 4.09 r_work: 0.2917 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26376 Z= 0.097 Angle : 0.523 10.374 35708 Z= 0.261 Chirality : 0.040 0.276 4005 Planarity : 0.003 0.062 4517 Dihedral : 8.169 165.781 3615 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.14 % Allowed : 19.50 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3137 helix: 1.30 (0.15), residues: 1258 sheet: -0.19 (0.26), residues: 426 loop : 0.08 (0.17), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 514 TYR 0.013 0.001 TYR C 482 PHE 0.030 0.001 PHE A 759 TRP 0.006 0.001 TRP C 350 HIS 0.021 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00225 (26375) covalent geometry : angle 0.52300 (35706) SS BOND : bond 0.00295 ( 1) SS BOND : angle 0.95497 ( 2) hydrogen bonds : bond 0.02688 ( 950) hydrogen bonds : angle 4.00620 ( 2664) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 135 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8973 (ppp) cc_final: 0.8258 (ppp) REVERT: E 462 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8636 (pmm) REVERT: F 626 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.4030 (m-80) REVERT: F 717 MET cc_start: -0.0383 (OUTLIER) cc_final: -0.1101 (mtp) REVERT: A 618 MET cc_start: 0.8844 (ptp) cc_final: 0.8516 (mtm) REVERT: B 649 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8950 (mmmm) REVERT: B 747 PHE cc_start: 0.7130 (t80) cc_final: 0.6487 (t80) REVERT: C 152 ARG cc_start: 0.9313 (ttm-80) cc_final: 0.8688 (tpt-90) REVERT: C 156 GLU cc_start: 0.8806 (mm-30) cc_final: 0.7857 (mm-30) REVERT: C 197 MET cc_start: 0.7868 (tpp) cc_final: 0.7247 (tpp) REVERT: C 219 TYR cc_start: 0.7788 (t80) cc_final: 0.6931 (t80) REVERT: C 462 MET cc_start: 0.9245 (mmm) cc_final: 0.8971 (mmm) REVERT: D 321 LEU cc_start: 0.8365 (tt) cc_final: 0.8130 (mm) REVERT: D 377 LYS cc_start: 0.9146 (OUTLIER) cc_final: 0.8895 (pptt) REVERT: D 717 MET cc_start: 0.9079 (mmm) cc_final: 0.8575 (mmm) REVERT: D 776 TYR cc_start: 0.8872 (m-80) cc_final: 0.8530 (m-80) outliers start: 62 outliers final: 48 residues processed: 187 average time/residue: 0.1900 time to fit residues: 56.1033 Evaluate side-chains 185 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 717 MET Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 722 LYS Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 554 PHE Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 754 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 260 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.102681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.064435 restraints weight = 92881.399| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 4.08 r_work: 0.2903 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26376 Z= 0.110 Angle : 0.525 9.098 35708 Z= 0.264 Chirality : 0.040 0.208 4005 Planarity : 0.003 0.062 4517 Dihedral : 8.034 164.875 3615 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.17 % Allowed : 19.57 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.16), residues: 3137 helix: 1.30 (0.15), residues: 1259 sheet: -0.18 (0.26), residues: 426 loop : 0.07 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 514 TYR 0.015 0.001 TYR C 482 PHE 0.023 0.001 PHE A 752 TRP 0.005 0.001 TRP C 350 HIS 0.005 0.001 HIS A 754 Details of bonding type rmsd covalent geometry : bond 0.00259 (26375) covalent geometry : angle 0.52521 (35706) SS BOND : bond 0.00277 ( 1) SS BOND : angle 0.96714 ( 2) hydrogen bonds : bond 0.02861 ( 950) hydrogen bonds : angle 4.04140 ( 2664) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8938 (ppp) cc_final: 0.8245 (ppp) REVERT: E 462 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8703 (pmm) REVERT: F 538 LYS cc_start: 0.8632 (pptt) cc_final: 0.8292 (pttp) REVERT: F 626 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.3926 (m-80) REVERT: F 717 MET cc_start: -0.0377 (OUTLIER) cc_final: -0.1098 (mtp) REVERT: A 618 MET cc_start: 0.8852 (ptp) cc_final: 0.8516 (mtm) REVERT: B 649 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8957 (mmmm) REVERT: B 747 PHE cc_start: 0.7024 (t80) cc_final: 0.6357 (t80) REVERT: C 152 ARG cc_start: 0.9319 (ttm-80) cc_final: 0.8901 (ptm-80) REVERT: C 156 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8531 (mm-30) REVERT: C 197 MET cc_start: 0.7785 (tpp) cc_final: 0.7166 (tpp) REVERT: C 219 TYR cc_start: 0.7892 (t80) cc_final: 0.7000 (t80) REVERT: C 462 MET cc_start: 0.9281 (mmm) cc_final: 0.8985 (mmm) REVERT: D 377 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8911 (pptt) REVERT: D 426 MET cc_start: 0.9291 (ttp) cc_final: 0.8771 (tmm) REVERT: D 717 MET cc_start: 0.9071 (mmm) cc_final: 0.8516 (mmm) REVERT: D 755 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8682 (p0) REVERT: D 764 LYS cc_start: 0.9206 (tppt) cc_final: 0.8867 (tppt) REVERT: D 776 TYR cc_start: 0.8859 (m-80) cc_final: 0.8506 (m-80) outliers start: 63 outliers final: 50 residues processed: 191 average time/residue: 0.1901 time to fit residues: 57.1793 Evaluate side-chains 189 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 133 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 774 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 717 MET Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 668 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 754 HIS Chi-restraints excluded: chain D residue 755 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 294 optimal weight: 7.9990 chunk 272 optimal weight: 0.5980 chunk 235 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 308 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 548 HIS ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.102159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.063232 restraints weight = 91037.896| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.15 r_work: 0.2865 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26376 Z= 0.172 Angle : 0.569 11.555 35708 Z= 0.287 Chirality : 0.042 0.200 4005 Planarity : 0.004 0.063 4517 Dihedral : 8.024 165.926 3615 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.14 % Allowed : 19.81 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 3137 helix: 1.20 (0.15), residues: 1261 sheet: -0.19 (0.26), residues: 438 loop : 0.02 (0.17), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 514 TYR 0.019 0.001 TYR C 482 PHE 0.033 0.001 PHE A 759 TRP 0.006 0.001 TRP D 350 HIS 0.004 0.001 HIS C 680 Details of bonding type rmsd covalent geometry : bond 0.00404 (26375) covalent geometry : angle 0.56944 (35706) SS BOND : bond 0.00246 ( 1) SS BOND : angle 1.05441 ( 2) hydrogen bonds : bond 0.03565 ( 950) hydrogen bonds : angle 4.26187 ( 2664) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6274 Ramachandran restraints generated. 3137 Oldfield, 0 Emsley, 3137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 458 MET cc_start: 0.8941 (ppp) cc_final: 0.8247 (ppp) REVERT: E 462 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8710 (pmm) REVERT: E 730 ASN cc_start: 0.7684 (t0) cc_final: 0.7469 (t0) REVERT: F 626 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.3770 (m-80) REVERT: F 717 MET cc_start: -0.0636 (OUTLIER) cc_final: -0.1413 (mtp) REVERT: A 372 ARG cc_start: 0.9592 (OUTLIER) cc_final: 0.9075 (ptp90) REVERT: A 618 MET cc_start: 0.8911 (ptp) cc_final: 0.8583 (mtm) REVERT: A 717 MET cc_start: 0.8040 (tpt) cc_final: 0.6727 (mmm) REVERT: B 747 PHE cc_start: 0.7054 (t80) cc_final: 0.6397 (t80) REVERT: C 152 ARG cc_start: 0.9309 (ttm-80) cc_final: 0.8888 (ptm-80) REVERT: C 156 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 197 MET cc_start: 0.7855 (tpp) cc_final: 0.7263 (tpp) REVERT: C 219 TYR cc_start: 0.7812 (t80) cc_final: 0.6940 (t80) REVERT: C 462 MET cc_start: 0.9317 (mmm) cc_final: 0.9022 (mmm) REVERT: D 377 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8997 (pptt) REVERT: D 426 MET cc_start: 0.9256 (ttp) cc_final: 0.8736 (tmm) REVERT: D 717 MET cc_start: 0.9057 (mmm) cc_final: 0.8474 (mmm) REVERT: D 755 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8750 (p0) REVERT: D 776 TYR cc_start: 0.8890 (m-80) cc_final: 0.8553 (m-80) outliers start: 62 outliers final: 49 residues processed: 189 average time/residue: 0.1825 time to fit residues: 54.8737 Evaluate side-chains 187 residues out of total 2903 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 132 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 548 HIS Chi-restraints excluded: chain E residue 713 HIS Chi-restraints excluded: chain E residue 731 VAL Chi-restraints excluded: chain E residue 734 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 601 ILE Chi-restraints excluded: chain F residue 626 PHE Chi-restraints excluded: chain F residue 663 ARG Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain F residue 717 MET Chi-restraints excluded: chain F residue 726 ILE Chi-restraints excluded: chain F residue 747 PHE Chi-restraints excluded: chain A residue 372 ARG Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 554 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 591 LYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 698 PHE Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 739 PHE Chi-restraints excluded: chain B residue 746 TYR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain C residue 605 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 757 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 357 PHE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 377 LYS Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 507 THR Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 740 GLN Chi-restraints excluded: chain D residue 754 HIS Chi-restraints excluded: chain D residue 755 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 310 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 191 optimal weight: 30.0000 chunk 89 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 293 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.102915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.064302 restraints weight = 90093.139| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 4.14 r_work: 0.2897 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26376 Z= 0.109 Angle : 0.546 10.125 35708 Z= 0.273 Chirality : 0.041 0.238 4005 Planarity : 0.003 0.063 4517 Dihedral : 7.890 166.820 3615 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 19.88 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 3137 helix: 1.25 (0.15), residues: 1252 sheet: -0.23 (0.27), residues: 426 loop : 0.07 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 551 TYR 0.015 0.001 TYR A 482 PHE 0.020 0.001 PHE A 778 TRP 0.006 0.001 TRP C 350 HIS 0.006 0.001 HIS E 548 Details of bonding type rmsd covalent geometry : bond 0.00257 (26375) covalent geometry : angle 0.54628 (35706) SS BOND : bond 0.00274 ( 1) SS BOND : angle 0.91161 ( 2) hydrogen bonds : bond 0.02926 ( 950) hydrogen bonds : angle 4.09361 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8459.24 seconds wall clock time: 145 minutes 20.23 seconds (8720.23 seconds total)