Starting phenix.real_space_refine on Sun Jun 22 15:02:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.map" model { file = "/net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwa_35051/06_2025/8hwa_35051.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "E" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "F" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.37, per 1000 atoms: 0.56 Number of scatterers: 25740 At special positions: 0 Unit cell: (125.925, 128.115, 173.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 76 " - pdb=" SG CYS E 385 " 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: 6.54 Conformation dependent library (CDL) restraints added in 3.1 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 42 sheets defined 42.3% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.689A pdb=" N ARG A 24 " --> pdb=" O PRO A 20 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 20 through 25' Processing helix chain 'A' and resid 36 through 47 removed outlier: 3.533A pdb=" N GLU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 105 removed outlier: 3.580A pdb=" N ILE A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 92 " --> pdb=" O ASP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.799A pdb=" N ASN A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.714A pdb=" N ARG A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 169 through 174 removed outlier: 6.152A pdb=" N ALA A 172 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 173 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 174 " --> pdb=" O THR A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 169 through 174' Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.805A pdb=" N ASP A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.716A pdb=" N LEU A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.601A pdb=" N ALA A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 314 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.515A pdb=" N SER A 381 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU A 382 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 384 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 398 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.184A pdb=" N LYS A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 455 through 469 Processing helix chain 'A' and resid 476 through 488 Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.918A 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 577 removed outlier: 3.734A pdb=" N ILE A 574 " --> pdb=" O ARG A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 619 removed outlier: 4.075A pdb=" N ARG A 619 " --> pdb=" O ASN A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 634 No H-bonds generated for 'chain 'A' and resid 632 through 634' Processing helix chain 'A' and resid 635 through 641 Processing helix chain 'A' and resid 653 through 660 removed outlier: 4.061A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 680 removed outlier: 3.706A pdb=" N PHE A 668 " --> pdb=" O TYR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 700 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 363 through 372 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 381 removed outlier: 3.695A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 385 through 398 Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.547A pdb=" N ASP B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS B 435 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.560A pdb=" N LYS B 450 " --> pdb=" O ASP B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 469 Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.767A pdb=" N ILE B 531 " --> pdb=" O GLY B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 570 through 577 removed outlier: 3.601A pdb=" N ILE B 574 " --> pdb=" O ARG B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 removed outlier: 3.784A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 634 No H-bonds generated for 'chain 'B' and resid 632 through 634' Processing helix chain 'B' and resid 635 through 641 Processing helix chain 'B' and resid 653 through 660 removed outlier: 3.963A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 660 " --> pdb=" O ASP B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 680 removed outlier: 3.507A pdb=" N PHE B 668 " --> pdb=" O TYR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 701 removed outlier: 3.868A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 336 Processing helix chain 'C' and resid 363 through 372 Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.962A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) 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 398 removed outlier: 3.516A pdb=" N ASP C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.539A pdb=" N ASP C 432 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C 435 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 Processing helix chain 'C' and resid 455 through 469 Processing helix chain 'C' and resid 475 through 488 Processing helix chain 'C' and resid 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 532 removed outlier: 3.808A pdb=" N ILE C 531 " --> pdb=" O GLY C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 570 through 577 removed outlier: 3.541A pdb=" N ILE C 574 " --> pdb=" O ARG C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 635 through 641 Processing helix chain 'C' and resid 653 through 660 removed outlier: 4.222A pdb=" N GLY C 657 " --> pdb=" O GLU C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 680 Processing helix chain 'C' and resid 689 through 692 removed outlier: 3.779A pdb=" N GLU C 692 " --> pdb=" O THR C 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 693 through 699 removed outlier: 3.819A pdb=" N TYR C 699 " --> pdb=" O ASP C 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 336 removed outlier: 3.675A pdb=" N ASN D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 376 through 381 removed outlier: 3.941A pdb=" N SER D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 384 No H-bonds generated for 'chain 'D' and resid 382 through 384' Processing helix chain 'D' and resid 385 through 398 removed outlier: 3.501A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 removed outlier: 4.312A pdb=" N LYS D 435 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 455 through 469 Processing helix chain 'D' and resid 475 through 488 Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.859A pdb=" N THR D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 529 through 534' Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 570 through 576 Processing helix chain 'D' and resid 614 through 619 removed outlier: 3.572A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 641 Processing helix chain 'D' and resid 653 through 660 removed outlier: 4.059A pdb=" N GLY D 657 " --> pdb=" O GLU D 653 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN D 660 " --> pdb=" O ASP D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 680 Processing helix chain 'D' and resid 689 through 692 removed outlier: 4.037A pdb=" N GLU D 692 " --> pdb=" O THR D 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 693 through 699 removed outlier: 3.809A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.618A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 376 through 381 removed outlier: 4.285A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 384 No H-bonds generated for 'chain 'E' and resid 382 through 384' Processing helix chain 'E' and resid 385 through 398 removed outlier: 3.558A pdb=" N ASP E 398 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 435 removed outlier: 4.075A pdb=" N LYS E 435 " --> pdb=" O ASP E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 451 removed outlier: 3.531A pdb=" N LYS E 450 " --> pdb=" O ASP E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 469 Processing helix chain 'E' and resid 472 through 474 No H-bonds generated for 'chain 'E' and resid 472 through 474' Processing helix chain 'E' and resid 475 through 488 removed outlier: 3.569A pdb=" N ARG E 479 " --> pdb=" O ASN E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.637A pdb=" N ALA E 545 " --> pdb=" O ASN E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 577 removed outlier: 3.621A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 619 removed outlier: 4.016A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 634 No H-bonds generated for 'chain 'E' and resid 632 through 634' Processing helix chain 'E' and resid 635 through 642 Processing helix chain 'E' and resid 654 through 661 removed outlier: 3.744A pdb=" N GLN E 660 " --> pdb=" O ASP E 656 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 680 removed outlier: 3.549A pdb=" N PHE E 668 " --> pdb=" O TYR E 664 " (cutoff:3.500A) Processing helix chain 'E' and resid 689 through 692 removed outlier: 4.035A pdb=" N GLU E 692 " --> pdb=" O THR E 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 689 through 692' Processing helix chain 'E' and resid 693 through 698 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.757A pdb=" N GLN F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 78 through 104 removed outlier: 3.977A pdb=" N GLN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP F 88 " --> pdb=" O THR F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 removed outlier: 4.376A pdb=" N ASN F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.503A pdb=" N LYS F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 168 Processing helix chain 'F' and resid 203 through 207 removed outlier: 3.538A pdb=" N TYR F 207 " --> pdb=" O ILE F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 231 Processing helix chain 'F' and resid 242 through 254 removed outlier: 3.511A pdb=" N ILE F 253 " --> pdb=" O ARG F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 264 Processing helix chain 'F' and resid 324 through 336 removed outlier: 3.866A pdb=" N ASN F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 Processing helix chain 'F' and resid 373 through 375 No H-bonds generated for 'chain 'F' and resid 373 through 375' Processing helix chain 'F' and resid 376 through 383 removed outlier: 4.869A pdb=" N SER F 381 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 398 removed outlier: 3.520A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 435 removed outlier: 4.208A pdb=" N LYS F 435 " --> pdb=" O ASP F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 469 Processing helix chain 'F' and resid 472 through 474 No H-bonds generated for 'chain 'F' and resid 472 through 474' Processing helix chain 'F' and resid 475 through 488 Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'F' and resid 528 through 532 removed outlier: 3.777A pdb=" N ILE F 531 " --> pdb=" O GLY F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 541 through 546 removed outlier: 3.557A pdb=" N ALA F 545 " --> pdb=" O ASN F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 577 removed outlier: 3.725A pdb=" N ILE F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 removed outlier: 3.538A pdb=" N ARG F 619 " --> pdb=" O ASN F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 634 No H-bonds generated for 'chain 'F' and resid 632 through 634' Processing helix chain 'F' and resid 635 through 641 removed outlier: 3.523A pdb=" N ASN F 641 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 659 Processing helix chain 'F' and resid 664 through 680 Processing helix chain 'F' and resid 689 through 692 Processing helix chain 'F' and resid 693 through 699 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 20 through 27 Processing helix chain 'K' and resid 36 through 47 removed outlier: 3.550A pdb=" N GLU K 41 " --> pdb=" O CYS K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 104 Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.643A pdb=" N VAL K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASN K 119 " --> pdb=" O SER K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 159 removed outlier: 4.710A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 168 Processing helix chain 'K' and resid 203 through 207 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 removed outlier: 3.568A pdb=" N GLU A 33 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 13 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 12 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 73 removed outlier: 6.927A pdb=" N THR A 140 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N MET A 69 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N LEU A 138 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N VAL A 71 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 136 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LEU A 73 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N HIS A 134 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N SER A 132 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 125 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N HIS A 134 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 73 removed outlier: 6.927A pdb=" N THR A 140 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N MET A 69 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.996A pdb=" N LEU A 138 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N VAL A 71 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ILE A 136 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N LEU A 73 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N HIS A 134 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR A 219 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.567A pdb=" N TYR A 306 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.567A pdb=" N TYR A 306 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA7, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.592A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.856A pdb=" N VAL A 525 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N SER A 556 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL A 553 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR A 499 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 604 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE A 501 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 582 removed outlier: 3.893A pdb=" N ASN A 594 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 629 through 630 removed outlier: 6.839A pdb=" N HIS A 629 " --> pdb=" O LYS A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.577A pdb=" N LEU B 340 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.673A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 525 through 526 removed outlier: 6.910A pdb=" N VAL B 525 " --> pdb=" O PHE B 554 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) removed outlier: 3.562A 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: 7.603A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AB6, first strand: chain 'B' and resid 629 through 631 Processing sheet with id=AB7, first strand: chain 'C' and resid 340 through 341 Processing sheet with id=AB8, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.910A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 419 " --> pdb=" O TYR C 428 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 525 through 526 removed outlier: 6.204A pdb=" N VAL C 553 " --> pdb=" O ILE C 601 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASP C 603 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N CYS C 555 " --> pdb=" O ASP C 603 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AC2, first strand: chain 'C' and resid 629 through 631 removed outlier: 6.883A pdb=" N HIS C 629 " --> pdb=" O LYS C 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 340 through 341 removed outlier: 3.518A pdb=" N ILE D 351 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.920A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 419 " --> pdb=" O TYR D 428 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 525 through 526 removed outlier: 6.991A pdb=" N VAL D 525 " --> pdb=" O PHE D 554 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N SER D 556 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL D 553 " --> pdb=" O ILE D 601 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ASP D 603 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS D 555 " --> pdb=" O ASP D 603 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 581 through 583 Processing sheet with id=AC7, first strand: chain 'D' and resid 629 through 631 Processing sheet with id=AC8, first strand: chain 'E' and resid 340 through 341 Processing sheet with id=AC9, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.776A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 525 through 527 removed outlier: 6.714A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 502 " --> pdb=" O VAL E 624 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 629 through 631 Processing sheet with id=AD3, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AD4, first strand: chain 'F' and resid 32 through 35 removed outlier: 3.625A pdb=" N GLU F 33 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N PHE F 12 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 64 through 73 removed outlier: 11.008A pdb=" N VAL F 65 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N ASP F 139 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE F 67 " --> pdb=" O PHE F 137 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 123 through 125 Processing sheet with id=AD7, first strand: chain 'F' and resid 294 through 299 removed outlier: 3.704A pdb=" N LYS F 317 " --> pdb=" O ILE F 305 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 340 through 341 Processing sheet with id=AD9, first strand: chain 'F' and resid 412 through 415 removed outlier: 3.678A pdb=" N GLY F 418 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 525 through 527 removed outlier: 6.022A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 628 through 631 removed outlier: 6.396A pdb=" N HIS F 629 " --> pdb=" O LYS F 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 7 through 8 Processing sheet with id=AE4, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.520A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE K 12 " --> pdb=" O SER K 55 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 64 through 73 removed outlier: 6.911A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 12.129A pdb=" N MET K 69 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 11.102A pdb=" N LEU K 138 " --> pdb=" O MET K 69 " (cutoff:3.500A) removed outlier: 12.121A pdb=" N VAL K 71 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 11.028A pdb=" N ILE K 136 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 12.810A pdb=" N LEU K 73 " --> pdb=" O HIS K 134 " (cutoff:3.500A) removed outlier: 11.645A pdb=" N HIS K 134 " --> pdb=" O LEU K 73 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 124 through 125 840 hydrogen bonds defined for protein. 2358 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: 9.20 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6095 1.33 - 1.45: 5196 1.45 - 1.57: 14744 1.57 - 1.70: 39 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" N ASP F 431 " pdb=" CA ASP F 431 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.88e+00 bond pdb=" N LEU B 700 " pdb=" CA LEU B 700 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.32e-02 5.74e+03 4.89e+00 bond pdb=" N ASP D 656 " pdb=" CA ASP D 656 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.33e-02 5.65e+03 4.83e+00 bond pdb=" N LEU C 700 " pdb=" CA LEU C 700 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.50e-02 4.44e+03 4.60e+00 bond pdb=" N ASP A 277 " pdb=" CA ASP A 277 " ideal model delta sigma weight residual 1.454 1.480 -0.026 1.21e-02 6.83e+03 4.52e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 35278 2.51 - 5.03: 278 5.03 - 7.54: 32 7.54 - 10.06: 3 10.06 - 12.57: 2 Bond angle restraints: 35593 Sorted by residual: angle pdb=" N LEU B 700 " pdb=" CA LEU B 700 " pdb=" C LEU B 700 " ideal model delta sigma weight residual 113.50 107.98 5.52 1.23e+00 6.61e-01 2.01e+01 angle pdb=" N LEU C 700 " pdb=" CA LEU C 700 " pdb=" C LEU C 700 " ideal model delta sigma weight residual 114.39 108.05 6.34 1.45e+00 4.76e-01 1.91e+01 angle pdb=" CB MET F 116 " pdb=" CG MET F 116 " pdb=" SD MET F 116 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N LEU E 700 " pdb=" CA LEU E 700 " pdb=" C LEU E 700 " ideal model delta sigma weight residual 113.37 107.87 5.50 1.38e+00 5.25e-01 1.59e+01 angle pdb=" CA GLU E 557 " pdb=" CB GLU E 557 " pdb=" CG GLU E 557 " ideal model delta sigma weight residual 114.10 121.52 -7.42 2.00e+00 2.50e-01 1.38e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 15428 31.32 - 62.64: 656 62.64 - 93.95: 46 93.95 - 125.27: 0 125.27 - 156.59: 2 Dihedral angle restraints: 16132 sinusoidal: 6841 harmonic: 9291 Sorted by residual: dihedral pdb=" CB CYS A 76 " pdb=" SG CYS A 76 " pdb=" SG CYS E 385 " pdb=" CB CYS E 385 " ideal model delta sinusoidal sigma weight residual -86.00 -23.24 -62.76 1 1.00e+01 1.00e-02 5.21e+01 dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.41 156.59 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.24 152.76 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 16129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2714 0.036 - 0.073: 908 0.073 - 0.109: 308 0.109 - 0.145: 50 0.145 - 0.182: 4 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU B 700 " pdb=" N LEU B 700 " pdb=" C LEU B 700 " pdb=" CB LEU B 700 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CB ILE F 681 " pdb=" CA ILE F 681 " pdb=" CG1 ILE F 681 " pdb=" CG2 ILE F 681 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA LEU E 700 " pdb=" N LEU E 700 " pdb=" C LEU E 700 " pdb=" CB LEU E 700 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 236 " 0.019 2.00e-02 2.50e+03 3.81e-02 1.46e+01 pdb=" C TRP A 236 " -0.066 2.00e-02 2.50e+03 pdb=" O TRP A 236 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 237 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 361 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A 362 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 375 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO F 376 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 376 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 376 " 0.030 5.00e-02 4.00e+02 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 180 2.55 - 3.13: 19464 3.13 - 3.72: 38400 3.72 - 4.31: 51885 4.31 - 4.90: 87277 Nonbonded interactions: 197206 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.956 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 2.005 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.023 2.170 nonbonded pdb=" O1A ATP D1001 " pdb="MG MG D1002 " model vdw 2.031 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.044 2.170 ... (remaining 197201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 700) selection = chain 'F' } ncs_group { reference = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = (chain 'D' and resid 323 through 701) selection = (chain 'E' and resid 323 through 701) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 55.140 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26282 Z= 0.130 Angle : 0.584 12.570 35595 Z= 0.329 Chirality : 0.041 0.182 3984 Planarity : 0.004 0.058 4537 Dihedral : 16.332 156.590 10087 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 0.35 % Allowed : 15.50 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 3133 helix: 0.54 (0.16), residues: 1073 sheet: -1.39 (0.25), residues: 454 loop : -1.48 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 350 HIS 0.003 0.000 HIS B 629 PHE 0.018 0.001 PHE D 698 TYR 0.020 0.001 TYR D 664 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.21464 ( 836) hydrogen bonds : angle 6.86020 ( 2358) SS BOND : bond 0.00028 ( 1) SS BOND : angle 4.99716 ( 2) covalent geometry : bond 0.00259 (26281) covalent geometry : angle 0.58266 (35593) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 225 time to evaluate : 2.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 684 MET cc_start: 0.8370 (tmm) cc_final: 0.7876 (tmm) REVERT: F 138 LEU cc_start: 0.7020 (mp) cc_final: 0.6584 (pt) REVERT: F 322 ASP cc_start: 0.7504 (t70) cc_final: 0.7051 (t70) REVERT: F 684 MET cc_start: 0.7655 (tpp) cc_final: 0.6494 (tpp) outliers start: 10 outliers final: 1 residues processed: 231 average time/residue: 0.3951 time to fit residues: 141.8443 Evaluate side-chains 203 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 419 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 662 ASN E 529 GLN ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 ASN ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 641 ASN ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.079194 restraints weight = 57212.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.082323 restraints weight = 31907.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082972 restraints weight = 19395.290| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 26282 Z= 0.268 Angle : 0.643 8.658 35595 Z= 0.335 Chirality : 0.046 0.175 3984 Planarity : 0.005 0.064 4537 Dihedral : 10.115 157.758 3668 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 2.77 % Allowed : 14.67 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3133 helix: 0.17 (0.15), residues: 1126 sheet: -1.53 (0.24), residues: 462 loop : -1.64 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 350 HIS 0.006 0.001 HIS F 680 PHE 0.021 0.002 PHE F 630 TYR 0.028 0.002 TYR C 482 ARG 0.008 0.001 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.04708 ( 836) hydrogen bonds : angle 5.19245 ( 2358) SS BOND : bond 0.00060 ( 1) SS BOND : angle 2.59146 ( 2) covalent geometry : bond 0.00634 (26281) covalent geometry : angle 0.64273 (35593) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 217 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8163 (t0) cc_final: 0.7889 (t70) REVERT: B 534 ASP cc_start: 0.8515 (t0) cc_final: 0.8313 (t0) REVERT: C 471 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9301 (pp) REVERT: D 660 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: E 382 GLU cc_start: 0.7551 (mp0) cc_final: 0.7196 (mp0) REVERT: E 660 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: F 109 HIS cc_start: 0.7348 (t-90) cc_final: 0.7071 (t70) REVERT: F 194 ILE cc_start: 0.8975 (pt) cc_final: 0.8656 (mm) REVERT: F 321 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8697 (pp) REVERT: F 322 ASP cc_start: 0.7851 (t70) cc_final: 0.7448 (t70) REVERT: F 332 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8130 (ttm-80) REVERT: K 40 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 80 outliers final: 50 residues processed: 281 average time/residue: 0.3652 time to fit residues: 162.8510 Evaluate side-chains 238 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain C residue 701 LYS Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 308 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 246 optimal weight: 0.4980 chunk 24 optimal weight: 5.9990 chunk 303 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN B 328 ASN B 466 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 548 HIS F 661 ASN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081757 restraints weight = 56542.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085047 restraints weight = 30671.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085808 restraints weight = 18418.160| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26282 Z= 0.118 Angle : 0.519 9.985 35595 Z= 0.269 Chirality : 0.042 0.172 3984 Planarity : 0.004 0.061 4537 Dihedral : 9.783 157.210 3667 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.26 % Allowed : 14.71 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3133 helix: 0.38 (0.16), residues: 1143 sheet: -1.34 (0.24), residues: 478 loop : -1.47 (0.15), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.008 0.001 HIS A 195 PHE 0.013 0.001 PHE D 698 TYR 0.017 0.001 TYR A 482 ARG 0.006 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 836) hydrogen bonds : angle 4.65962 ( 2358) SS BOND : bond 0.00236 ( 1) SS BOND : angle 1.79981 ( 2) covalent geometry : bond 0.00276 (26281) covalent geometry : angle 0.51853 (35593) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 213 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7417 (ttp80) REVERT: A 534 ASP cc_start: 0.8075 (t0) cc_final: 0.7790 (t70) REVERT: B 507 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8998 (m) REVERT: B 534 ASP cc_start: 0.8497 (t0) cc_final: 0.8287 (t0) REVERT: C 471 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9279 (pp) REVERT: C 579 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 522 ASP cc_start: 0.8567 (t70) cc_final: 0.8277 (t0) REVERT: E 382 GLU cc_start: 0.7538 (mp0) cc_final: 0.7102 (mp0) REVERT: E 426 MET cc_start: 0.7220 (mmm) cc_final: 0.6982 (mmm) REVERT: E 529 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7852 (pp30) REVERT: E 560 ASP cc_start: 0.7261 (t0) cc_final: 0.7039 (t0) REVERT: E 660 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8374 (mp10) REVERT: F 322 ASP cc_start: 0.7657 (t70) cc_final: 0.7242 (t70) REVERT: F 332 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8249 (ttm-80) outliers start: 94 outliers final: 46 residues processed: 289 average time/residue: 0.3661 time to fit residues: 170.6404 Evaluate side-chains 245 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 194 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 72 optimal weight: 0.9980 chunk 176 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 270 optimal weight: 0.0870 chunk 274 optimal weight: 10.0000 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 HIS ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** K 109 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 = 0.3533 r_free = 0.3533 target = 0.109037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.081543 restraints weight = 56975.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084704 restraints weight = 30928.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085620 restraints weight = 18728.662| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26282 Z= 0.133 Angle : 0.521 9.717 35595 Z= 0.269 Chirality : 0.042 0.171 3984 Planarity : 0.004 0.058 4537 Dihedral : 9.532 157.650 3667 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 3.16 % Allowed : 15.44 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3133 helix: 0.48 (0.16), residues: 1144 sheet: -1.25 (0.24), residues: 478 loop : -1.45 (0.15), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 350 HIS 0.002 0.001 HIS K 195 PHE 0.011 0.001 PHE F 261 TYR 0.018 0.001 TYR A 482 ARG 0.004 0.000 ARG B 612 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 836) hydrogen bonds : angle 4.51503 ( 2358) SS BOND : bond 0.00001 ( 1) SS BOND : angle 1.13294 ( 2) covalent geometry : bond 0.00314 (26281) covalent geometry : angle 0.52109 (35593) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 205 time to evaluate : 2.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7281 (ttp80) REVERT: A 534 ASP cc_start: 0.8124 (t0) cc_final: 0.7775 (t70) REVERT: B 507 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9020 (m) REVERT: B 534 ASP cc_start: 0.8518 (t0) cc_final: 0.8291 (t0) REVERT: B 572 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: C 471 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9280 (pp) REVERT: D 367 LEU cc_start: 0.9310 (tt) cc_final: 0.9039 (tp) REVERT: D 522 ASP cc_start: 0.8571 (t70) cc_final: 0.8260 (t0) REVERT: D 660 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: E 382 GLU cc_start: 0.7533 (mp0) cc_final: 0.7074 (mp0) REVERT: E 426 MET cc_start: 0.7236 (mmm) cc_final: 0.7002 (mmm) REVERT: E 560 ASP cc_start: 0.7443 (t0) cc_final: 0.7196 (t0) REVERT: E 660 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8390 (mp10) REVERT: F 180 LEU cc_start: 0.7978 (tt) cc_final: 0.7478 (mt) REVERT: F 288 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8593 (tpt90) REVERT: F 321 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8580 (pp) REVERT: F 322 ASP cc_start: 0.7667 (t70) cc_final: 0.7278 (t70) REVERT: F 332 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8282 (ttm-80) REVERT: F 547 MET cc_start: 0.8463 (ttm) cc_final: 0.8188 (ttm) REVERT: F 684 MET cc_start: 0.7970 (tpp) cc_final: 0.7306 (tpp) REVERT: K 40 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8428 (tt) outliers start: 91 outliers final: 60 residues processed: 280 average time/residue: 0.3767 time to fit residues: 168.5033 Evaluate side-chains 264 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 157 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 281 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 292 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 478 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 661 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080021 restraints weight = 57065.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.083023 restraints weight = 31603.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083997 restraints weight = 19550.886| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26282 Z= 0.186 Angle : 0.554 11.153 35595 Z= 0.286 Chirality : 0.043 0.191 3984 Planarity : 0.004 0.058 4537 Dihedral : 9.477 158.082 3667 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 3.54 % Allowed : 16.09 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3133 helix: 0.54 (0.16), residues: 1126 sheet: -1.31 (0.24), residues: 485 loop : -1.42 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.017 0.001 HIS A 195 PHE 0.013 0.001 PHE F 261 TYR 0.022 0.001 TYR A 482 ARG 0.003 0.000 ARG F 665 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 836) hydrogen bonds : angle 4.55891 ( 2358) SS BOND : bond 0.00469 ( 1) SS BOND : angle 0.88927 ( 2) covalent geometry : bond 0.00441 (26281) covalent geometry : angle 0.55378 (35593) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 200 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5463 (OUTLIER) cc_final: 0.4972 (p0) REVERT: A 99 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7212 (ttp80) REVERT: A 150 MET cc_start: 0.9190 (ttm) cc_final: 0.8908 (ttt) REVERT: A 523 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8822 (mt) REVERT: A 534 ASP cc_start: 0.8061 (t70) cc_final: 0.7779 (t70) REVERT: B 507 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.9028 (m) REVERT: B 534 ASP cc_start: 0.8539 (t0) cc_final: 0.8338 (t0) REVERT: B 572 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: C 471 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9288 (pp) REVERT: D 522 ASP cc_start: 0.8574 (t70) cc_final: 0.8250 (t0) REVERT: D 660 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7531 (mp10) REVERT: E 382 GLU cc_start: 0.7545 (mp0) cc_final: 0.7071 (mp0) REVERT: E 426 MET cc_start: 0.7310 (mmm) cc_final: 0.7055 (mmm) REVERT: E 660 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8389 (mp10) REVERT: F 288 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8609 (tpt90) REVERT: F 321 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8658 (pp) REVERT: F 322 ASP cc_start: 0.7836 (t70) cc_final: 0.7471 (t70) REVERT: F 332 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8242 (ttm-80) REVERT: K 40 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8456 (tt) outliers start: 102 outliers final: 70 residues processed: 286 average time/residue: 0.3677 time to fit residues: 167.8243 Evaluate side-chains 265 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 184 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 131 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 250 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 478 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN F 109 HIS F 198 GLN ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS F 661 ASN ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.082716 restraints weight = 56372.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085691 restraints weight = 30926.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086940 restraints weight = 19056.827| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 26282 Z= 0.099 Angle : 0.506 11.053 35595 Z= 0.261 Chirality : 0.041 0.171 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.219 157.443 3667 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.42 % Favored : 96.52 % Rotamer: Outliers : 2.81 % Allowed : 17.41 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3133 helix: 0.60 (0.16), residues: 1153 sheet: -1.14 (0.25), residues: 481 loop : -1.28 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.009 0.001 HIS F 629 PHE 0.010 0.001 PHE F 630 TYR 0.020 0.001 TYR A 482 ARG 0.003 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.02916 ( 836) hydrogen bonds : angle 4.24100 ( 2358) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.63974 ( 2) covalent geometry : bond 0.00229 (26281) covalent geometry : angle 0.50611 (35593) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 223 time to evaluate : 3.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5560 (OUTLIER) cc_final: 0.4980 (p0) REVERT: A 99 ARG cc_start: 0.7875 (ttp80) cc_final: 0.7247 (ttp80) REVERT: A 534 ASP cc_start: 0.8047 (t70) cc_final: 0.7673 (t70) REVERT: B 507 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9003 (m) REVERT: B 572 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: C 382 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7636 (tp30) REVERT: C 471 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9281 (pp) REVERT: D 367 LEU cc_start: 0.9274 (tt) cc_final: 0.8967 (tp) REVERT: D 522 ASP cc_start: 0.8526 (t70) cc_final: 0.8232 (t0) REVERT: D 660 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7439 (mp10) REVERT: E 382 GLU cc_start: 0.7532 (mp0) cc_final: 0.7050 (mp0) REVERT: E 426 MET cc_start: 0.7246 (mmm) cc_final: 0.7007 (mmm) REVERT: E 660 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8411 (mp10) REVERT: F 180 LEU cc_start: 0.7955 (tt) cc_final: 0.7435 (mt) REVERT: F 288 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8588 (mmm160) outliers start: 81 outliers final: 55 residues processed: 289 average time/residue: 0.4026 time to fit residues: 185.0085 Evaluate side-chains 259 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 623 VAL Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 268 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 116 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN A 641 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.107763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.079639 restraints weight = 57253.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082202 restraints weight = 31451.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083858 restraints weight = 21588.979| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26282 Z= 0.185 Angle : 0.572 10.977 35595 Z= 0.292 Chirality : 0.043 0.200 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.333 158.658 3667 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.02 % Rotamer: Outliers : 3.30 % Allowed : 17.79 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3133 helix: 0.68 (0.16), residues: 1134 sheet: -1.26 (0.24), residues: 495 loop : -1.31 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.004 0.001 HIS F 347 PHE 0.013 0.001 PHE D 626 TYR 0.029 0.001 TYR A 482 ARG 0.004 0.000 ARG A 479 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 836) hydrogen bonds : angle 4.40508 ( 2358) SS BOND : bond 0.00362 ( 1) SS BOND : angle 0.78330 ( 2) covalent geometry : bond 0.00442 (26281) covalent geometry : angle 0.57155 (35593) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 197 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5417 (OUTLIER) cc_final: 0.4886 (p0) REVERT: A 447 ASP cc_start: 0.7900 (t0) cc_final: 0.7666 (t0) REVERT: A 534 ASP cc_start: 0.7968 (t70) cc_final: 0.7670 (t70) REVERT: B 507 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9050 (m) REVERT: B 572 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8295 (m-30) REVERT: C 382 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7803 (tp30) REVERT: C 471 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9294 (pp) REVERT: D 367 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9148 (tp) REVERT: D 522 ASP cc_start: 0.8495 (t70) cc_final: 0.8195 (t0) REVERT: D 660 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: E 382 GLU cc_start: 0.7495 (mp0) cc_final: 0.6997 (mp0) REVERT: E 426 MET cc_start: 0.7383 (mmm) cc_final: 0.7111 (mmm) REVERT: E 660 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: F 288 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8599 (tpt90) REVERT: F 332 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8232 (ttm-80) REVERT: F 554 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6175 (m-80) outliers start: 95 outliers final: 69 residues processed: 275 average time/residue: 0.3784 time to fit residues: 165.9520 Evaluate side-chains 272 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 193 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 298 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 285 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 218 optimal weight: 30.0000 chunk 264 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 118 optimal weight: 0.0570 chunk 246 optimal weight: 4.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 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 = 0.3516 r_free = 0.3516 target = 0.107828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.080297 restraints weight = 56986.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083446 restraints weight = 31374.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084266 restraints weight = 18937.377| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26282 Z= 0.165 Angle : 0.560 11.966 35595 Z= 0.287 Chirality : 0.042 0.166 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.244 158.255 3667 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 3.36 % Allowed : 17.86 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3133 helix: 0.70 (0.16), residues: 1133 sheet: -1.25 (0.24), residues: 495 loop : -1.30 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.005 0.001 HIS F 629 PHE 0.012 0.001 PHE F 630 TYR 0.021 0.001 TYR A 482 ARG 0.008 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03461 ( 836) hydrogen bonds : angle 4.34834 ( 2358) SS BOND : bond 0.00298 ( 1) SS BOND : angle 0.69366 ( 2) covalent geometry : bond 0.00393 (26281) covalent geometry : angle 0.56048 (35593) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 211 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5483 (OUTLIER) cc_final: 0.4954 (p0) REVERT: A 447 ASP cc_start: 0.7935 (t0) cc_final: 0.7710 (t0) REVERT: A 523 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8812 (mt) REVERT: A 534 ASP cc_start: 0.8120 (t70) cc_final: 0.7717 (t70) REVERT: B 507 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9031 (m) REVERT: B 572 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: C 382 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7781 (tp30) REVERT: C 471 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9302 (pp) REVERT: C 557 GLU cc_start: 0.7503 (tp30) cc_final: 0.7171 (tp30) REVERT: D 367 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9101 (tp) REVERT: D 522 ASP cc_start: 0.8519 (t70) cc_final: 0.8139 (t0) REVERT: D 575 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8541 (mtpp) REVERT: D 660 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: D 684 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7038 (tmm) REVERT: E 382 GLU cc_start: 0.7449 (mp0) cc_final: 0.6948 (mp0) REVERT: E 426 MET cc_start: 0.7375 (mmm) cc_final: 0.7102 (mmm) REVERT: E 660 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: F 288 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8625 (tpt90) REVERT: F 332 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8293 (ttm-80) REVERT: F 554 PHE cc_start: 0.6677 (OUTLIER) cc_final: 0.6153 (m-80) outliers start: 97 outliers final: 73 residues processed: 291 average time/residue: 0.3724 time to fit residues: 173.3322 Evaluate side-chains 282 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 214 MET Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 266 optimal weight: 7.9990 chunk 308 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 255 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS ** F 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 HIS ** 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 = 0.3509 r_free = 0.3509 target = 0.107333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079863 restraints weight = 57287.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.083159 restraints weight = 31805.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083883 restraints weight = 18987.451| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26282 Z= 0.189 Angle : 0.591 12.895 35595 Z= 0.301 Chirality : 0.043 0.248 3984 Planarity : 0.004 0.061 4537 Dihedral : 9.252 158.970 3667 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.92 % Rotamer: Outliers : 3.43 % Allowed : 18.28 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3133 helix: 0.65 (0.16), residues: 1133 sheet: -1.29 (0.24), residues: 487 loop : -1.30 (0.15), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.004 0.001 HIS F 347 PHE 0.014 0.001 PHE A 240 TYR 0.022 0.001 TYR A 482 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 836) hydrogen bonds : angle 4.42245 ( 2358) SS BOND : bond 0.00378 ( 1) SS BOND : angle 0.71307 ( 2) covalent geometry : bond 0.00450 (26281) covalent geometry : angle 0.59062 (35593) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 198 time to evaluate : 2.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5614 (OUTLIER) cc_final: 0.5123 (p0) REVERT: A 447 ASP cc_start: 0.7938 (t0) cc_final: 0.7715 (t0) REVERT: A 523 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8770 (mt) REVERT: A 534 ASP cc_start: 0.8124 (t70) cc_final: 0.7713 (t70) REVERT: B 507 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.9033 (m) REVERT: B 572 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8312 (m-30) REVERT: C 382 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7699 (tp30) REVERT: C 471 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9297 (pp) REVERT: D 367 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9151 (tp) REVERT: D 522 ASP cc_start: 0.8523 (t70) cc_final: 0.8134 (t0) REVERT: D 660 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7511 (mp10) REVERT: D 684 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7113 (tmm) REVERT: E 382 GLU cc_start: 0.7473 (mp0) cc_final: 0.6984 (mp0) REVERT: E 426 MET cc_start: 0.7375 (mmm) cc_final: 0.7095 (mmm) REVERT: E 660 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: E 684 MET cc_start: 0.8534 (tmm) cc_final: 0.8086 (tmm) REVERT: F 288 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.8637 (tpt90) REVERT: F 332 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8232 (ttm-80) REVERT: F 399 MET cc_start: 0.8494 (mtt) cc_final: 0.8178 (mtt) REVERT: F 554 PHE cc_start: 0.6732 (OUTLIER) cc_final: 0.6220 (m-80) REVERT: K 1 MET cc_start: 0.2017 (tpt) cc_final: 0.1510 (tpt) outliers start: 99 outliers final: 79 residues processed: 279 average time/residue: 0.3627 time to fit residues: 160.9787 Evaluate side-chains 286 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 195 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 662 ASN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 651 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 CYS Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 485 THR Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 406 THR Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 69 optimal weight: 5.9990 chunk 153 optimal weight: 0.5980 chunk 98 optimal weight: 0.0670 chunk 13 optimal weight: 9.9990 chunk 119 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS A 478 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 629 HIS ** K 109 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 = 0.3549 r_free = 0.3549 target = 0.109852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082708 restraints weight = 56355.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.085670 restraints weight = 30683.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086742 restraints weight = 18757.698| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26282 Z= 0.101 Angle : 0.553 13.267 35595 Z= 0.280 Chirality : 0.041 0.250 3984 Planarity : 0.004 0.057 4537 Dihedral : 8.971 158.401 3667 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 2.53 % Allowed : 19.32 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3133 helix: 0.84 (0.16), residues: 1135 sheet: -1.12 (0.24), residues: 493 loop : -1.15 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.004 0.000 HIS K 109 PHE 0.030 0.001 PHE A 120 TYR 0.016 0.001 TYR B 482 ARG 0.006 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02866 ( 836) hydrogen bonds : angle 4.14517 ( 2358) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.60811 ( 2) covalent geometry : bond 0.00232 (26281) covalent geometry : angle 0.55311 (35593) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 3.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASN cc_start: 0.5550 (OUTLIER) cc_final: 0.5025 (p0) REVERT: A 534 ASP cc_start: 0.7980 (t70) cc_final: 0.7524 (t70) REVERT: B 507 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.9004 (m) REVERT: B 572 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: C 471 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9267 (pp) REVERT: C 607 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8124 (ttmt) REVERT: D 367 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9015 (tp) REVERT: D 502 PHE cc_start: 0.8524 (t80) cc_final: 0.8266 (t80) REVERT: D 522 ASP cc_start: 0.8480 (t70) cc_final: 0.8081 (t0) REVERT: D 660 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: D 684 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7047 (tmm) REVERT: E 382 GLU cc_start: 0.7548 (mp0) cc_final: 0.7029 (mp0) REVERT: E 426 MET cc_start: 0.7300 (mmm) cc_final: 0.7041 (mmm) REVERT: E 660 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8370 (mp10) REVERT: E 684 MET cc_start: 0.8470 (tmm) cc_final: 0.8067 (tmm) REVERT: F 288 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8549 (mmm160) REVERT: F 332 ARG cc_start: 0.8968 (OUTLIER) cc_final: 0.8305 (ttm-80) REVERT: F 502 PHE cc_start: 0.8250 (t80) cc_final: 0.7984 (t80) REVERT: F 554 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: K 1 MET cc_start: 0.2147 (tpt) cc_final: 0.1794 (tpt) outliers start: 73 outliers final: 55 residues processed: 281 average time/residue: 0.4045 time to fit residues: 183.6457 Evaluate side-chains 269 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 609 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 660 GLN Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain D residue 491 CYS Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain E residue 660 GLN Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 89 PHE Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 288 ARG Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 535 VAL Chi-restraints excluded: chain F residue 554 PHE Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 683 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ILE Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 55 optimal weight: 7.9990 chunk 240 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 0.0030 chunk 168 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 548 HIS ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS ** K 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.109961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082737 restraints weight = 56498.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085626 restraints weight = 30668.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086784 restraints weight = 18563.242| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 26282 Z= 0.105 Angle : 0.557 13.414 35595 Z= 0.281 Chirality : 0.041 0.248 3984 Planarity : 0.004 0.056 4537 Dihedral : 8.820 158.847 3667 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.70 % Favored : 96.27 % Rotamer: Outliers : 2.46 % Allowed : 19.60 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3133 helix: 0.96 (0.16), residues: 1117 sheet: -1.05 (0.24), residues: 491 loop : -1.09 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 350 HIS 0.004 0.001 HIS K 109 PHE 0.032 0.001 PHE A 120 TYR 0.016 0.001 TYR B 482 ARG 0.008 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 836) hydrogen bonds : angle 4.09161 ( 2358) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.46664 ( 2) covalent geometry : bond 0.00246 (26281) covalent geometry : angle 0.55735 (35593) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7301.56 seconds wall clock time: 128 minutes 15.25 seconds (7695.25 seconds total)