Starting phenix.real_space_refine on Mon Aug 25 06:55:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hwa_35051/08_2025/8hwa_35051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hwa_35051/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2025/8hwa_35051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2025/8hwa_35051.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2025/8hwa_35051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hwa_35051/08_2025/8hwa_35051.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 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: 5.08, per 1000 atoms: 0.20 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: 1.68 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.63 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: 3.54 Time building geometry restraints manager: 2.21 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.520 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (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 ARG 0.006 0.000 ARG A 99 TYR 0.020 0.001 TYR D 664 PHE 0.018 0.001 PHE D 698 TRP 0.008 0.001 TRP A 350 HIS 0.003 0.000 HIS B 629 Details of bonding type rmsd covalent geometry : bond 0.00259 (26281) covalent geometry : angle 0.58266 (35593) SS BOND : bond 0.00028 ( 1) SS BOND : angle 4.99716 ( 2) hydrogen bonds : bond 0.21464 ( 836) hydrogen bonds : angle 6.86020 ( 2358) *********************** 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 : 0.791 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: 0.1489 time to fit residues: 54.0293 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 : 0.742 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.0050 overall best weight: 1.9400 ------------------------------------------------------------------------------- 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 195 HIS ** A 478 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 ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 ASN ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 548 HIS ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.109711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.082018 restraints weight = 57195.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085127 restraints weight = 31301.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.086230 restraints weight = 18953.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086497 restraints weight = 16262.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086625 restraints weight = 14805.221| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26282 Z= 0.157 Angle : 0.547 8.306 35595 Z= 0.286 Chirality : 0.043 0.156 3984 Planarity : 0.004 0.062 4537 Dihedral : 9.937 156.873 3668 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.25 % Allowed : 14.15 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.15), residues: 3133 helix: 0.38 (0.16), residues: 1138 sheet: -1.35 (0.24), residues: 477 loop : -1.46 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.019 0.001 TYR A 482 PHE 0.017 0.001 PHE A 243 TRP 0.011 0.001 TRP A 350 HIS 0.004 0.001 HIS F 290 Details of bonding type rmsd covalent geometry : bond 0.00370 (26281) covalent geometry : angle 0.54667 (35593) SS BOND : bond 0.00165 ( 1) SS BOND : angle 2.44963 ( 2) hydrogen bonds : bond 0.03846 ( 836) hydrogen bonds : angle 4.95008 ( 2358) *********************** 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 292 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7754 (ttp80) cc_final: 0.7279 (ttp80) REVERT: A 534 ASP cc_start: 0.8155 (t0) cc_final: 0.7834 (t70) REVERT: B 534 ASP cc_start: 0.8503 (t0) cc_final: 0.8289 (t0) REVERT: C 471 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9264 (pp) REVERT: D 522 ASP cc_start: 0.8576 (t70) cc_final: 0.8308 (t0) REVERT: E 382 GLU cc_start: 0.7551 (mp0) cc_final: 0.7201 (mp0) REVERT: E 529 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7822 (pp30) REVERT: E 660 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: F 194 ILE cc_start: 0.8923 (pt) cc_final: 0.8546 (mm) REVERT: F 322 ASP cc_start: 0.7639 (t70) cc_final: 0.7233 (t70) REVERT: F 547 MET cc_start: 0.8576 (ttm) cc_final: 0.8292 (ttm) REVERT: F 684 MET cc_start: 0.8345 (tpp) cc_final: 0.7771 (tpp) REVERT: K 40 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8383 (tt) outliers start: 65 outliers final: 39 residues processed: 275 average time/residue: 0.1829 time to fit residues: 80.0182 Evaluate side-chains 241 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 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 497 CYS Chi-restraints excluded: chain B residue 505 THR 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 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 681 ILE Chi-restraints excluded: chain E residue 383 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 529 GLN Chi-restraints excluded: chain E residue 535 VAL Chi-restraints excluded: chain E residue 624 VAL 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 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 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 210 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 256 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 chunk 182 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 ASN D 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 GLN F 198 GLN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 661 ASN ** 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 = 0.3568 r_free = 0.3568 target = 0.111119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.083762 restraints weight = 56839.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086923 restraints weight = 30375.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.087786 restraints weight = 18466.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088273 restraints weight = 15853.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088437 restraints weight = 14502.564| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26282 Z= 0.100 Angle : 0.498 9.862 35595 Z= 0.258 Chirality : 0.041 0.182 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.638 156.797 3667 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.78 % Rotamer: Outliers : 2.39 % Allowed : 14.33 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.15), residues: 3133 helix: 0.56 (0.16), residues: 1136 sheet: -1.22 (0.24), residues: 481 loop : -1.38 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 612 TYR 0.014 0.001 TYR A 482 PHE 0.013 0.001 PHE D 698 TRP 0.009 0.001 TRP A 350 HIS 0.010 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00229 (26281) covalent geometry : angle 0.49771 (35593) SS BOND : bond 0.00263 ( 1) SS BOND : angle 1.72872 ( 2) hydrogen bonds : bond 0.03314 ( 836) hydrogen bonds : angle 4.56157 ( 2358) *********************** 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 297 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3107 (ttt) cc_final: 0.2896 (ttm) REVERT: A 534 ASP cc_start: 0.8173 (t0) cc_final: 0.7805 (t70) REVERT: B 534 ASP cc_start: 0.8440 (t0) cc_final: 0.8233 (t0) REVERT: C 471 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9247 (pp) REVERT: C 579 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 522 ASP cc_start: 0.8568 (t70) cc_final: 0.8300 (t0) REVERT: D 660 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7412 (mp10) REVERT: E 382 GLU cc_start: 0.7549 (mp0) cc_final: 0.7136 (mp0) REVERT: E 426 MET cc_start: 0.7143 (mmm) cc_final: 0.6916 (mmm) REVERT: E 660 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: F 180 LEU cc_start: 0.8057 (tt) cc_final: 0.7638 (mt) REVERT: F 194 ILE cc_start: 0.8924 (pt) cc_final: 0.8567 (mm) REVERT: F 322 ASP cc_start: 0.7559 (t70) cc_final: 0.7159 (t70) REVERT: F 332 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8179 (ttm-80) REVERT: F 547 MET cc_start: 0.8580 (ttm) cc_final: 0.8266 (ttm) REVERT: F 684 MET cc_start: 0.8415 (tpp) cc_final: 0.8129 (tpp) outliers start: 69 outliers final: 42 residues processed: 280 average time/residue: 0.1809 time to fit residues: 80.5278 Evaluate side-chains 244 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 1.074 ------------------------------------------------------------------------------- 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 195 HIS Chi-restraints excluded: chain A residue 212 VAL 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 340 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 486 LEU 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 609 VAL Chi-restraints excluded: chain C residue 632 GLN Chi-restraints excluded: chain C residue 660 GLN 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 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 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 280 THR Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 661 ASN Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 72 ASP 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 295 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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** ** A 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** 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 = 0.3484 r_free = 0.3484 target = 0.105888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.078205 restraints weight = 57025.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081040 restraints weight = 31752.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.082014 restraints weight = 19669.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082473 restraints weight = 17542.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082485 restraints weight = 15336.119| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 26282 Z= 0.295 Angle : 0.647 10.585 35595 Z= 0.336 Chirality : 0.046 0.180 3984 Planarity : 0.005 0.059 4537 Dihedral : 9.831 158.646 3667 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.71 % Favored : 94.22 % Rotamer: Outliers : 3.95 % Allowed : 15.02 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.15), residues: 3133 helix: 0.30 (0.15), residues: 1126 sheet: -1.47 (0.23), residues: 480 loop : -1.60 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 387 TYR 0.030 0.002 TYR C 482 PHE 0.019 0.002 PHE F 630 TRP 0.014 0.002 TRP A 350 HIS 0.006 0.001 HIS F 347 Details of bonding type rmsd covalent geometry : bond 0.00699 (26281) covalent geometry : angle 0.64725 (35593) SS BOND : bond 0.01015 ( 1) SS BOND : angle 0.67852 ( 2) hydrogen bonds : bond 0.04717 ( 836) hydrogen bonds : angle 4.93321 ( 2358) *********************** 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 317 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 203 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8067 (t70) cc_final: 0.7818 (t70) REVERT: B 534 ASP cc_start: 0.8518 (t0) cc_final: 0.8311 (t0) REVERT: B 572 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: C 471 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9305 (pp) REVERT: D 522 ASP cc_start: 0.8602 (t70) cc_final: 0.8241 (t0) REVERT: D 660 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: E 382 GLU cc_start: 0.7499 (mp0) cc_final: 0.7048 (mp0) REVERT: E 426 MET cc_start: 0.7345 (mmm) cc_final: 0.7093 (mmm) REVERT: E 660 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8379 (mp10) REVERT: F 288 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8613 (tpt90) REVERT: F 321 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8667 (pp) REVERT: F 322 ASP cc_start: 0.7873 (t70) cc_final: 0.7500 (t70) REVERT: K 40 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8459 (tt) outliers start: 114 outliers final: 71 residues processed: 301 average time/residue: 0.1684 time to fit residues: 81.6884 Evaluate side-chains 260 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 182 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 194 ILE Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 212 VAL 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 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 401 VAL Chi-restraints excluded: chain A residue 404 VAL 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 471 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS 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 624 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 486 LEU 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 349 VAL 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 632 GLN 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 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 363 LEU 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 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 116 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 0.0040 chunk 46 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 228 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.8996 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 GLN ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 109 HIS ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 541 ASN F 548 HIS K 25 GLN ** 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 = 0.3543 r_free = 0.3543 target = 0.109633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082270 restraints weight = 56338.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085273 restraints weight = 30508.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086092 restraints weight = 18879.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086578 restraints weight = 16507.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086735 restraints weight = 14996.613| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1670 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= 0.103 Angle : 0.518 11.129 35595 Z= 0.266 Chirality : 0.041 0.205 3984 Planarity : 0.004 0.057 4537 Dihedral : 9.349 157.035 3667 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.35 % Favored : 96.58 % Rotamer: Outliers : 2.60 % Allowed : 16.48 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.15), residues: 3133 helix: 0.52 (0.16), residues: 1145 sheet: -1.21 (0.24), residues: 483 loop : -1.37 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.016 0.001 TYR B 482 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP A 350 HIS 0.015 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00239 (26281) covalent geometry : angle 0.51754 (35593) SS BOND : bond 0.00157 ( 1) SS BOND : angle 0.77677 ( 2) hydrogen bonds : bond 0.03113 ( 836) hydrogen bonds : angle 4.38171 ( 2358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 218 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8158 (t70) cc_final: 0.7780 (t70) REVERT: B 534 ASP cc_start: 0.8486 (t0) cc_final: 0.8284 (t0) REVERT: C 382 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7742 (mm-30) REVERT: C 471 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9276 (pp) REVERT: C 557 GLU cc_start: 0.7703 (tp30) cc_final: 0.7201 (tp30) REVERT: D 522 ASP cc_start: 0.8482 (t70) cc_final: 0.8133 (t0) REVERT: D 575 LYS cc_start: 0.9014 (mtpp) cc_final: 0.8714 (mtpp) REVERT: D 660 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: E 382 GLU cc_start: 0.7509 (mp0) cc_final: 0.7028 (mp0) REVERT: E 426 MET cc_start: 0.7300 (mmm) cc_final: 0.7037 (mmm) REVERT: E 660 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: F 180 LEU cc_start: 0.8008 (tt) cc_final: 0.7527 (mt) REVERT: F 332 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8083 (ttm-80) REVERT: F 547 MET cc_start: 0.8485 (ttm) cc_final: 0.8217 (ttm) REVERT: F 684 MET cc_start: 0.7743 (tpp) cc_final: 0.6923 (tpp) outliers start: 75 outliers final: 53 residues processed: 280 average time/residue: 0.1721 time to fit residues: 76.5162 Evaluate side-chains 253 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 196 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 A residue 662 ASN Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL 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 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 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 D residue 351 ILE Chi-restraints excluded: chain D residue 486 LEU 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 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 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 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 472 THR Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 532 LEU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 229 optimal weight: 5.9990 chunk 270 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 203 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 ASN E 328 ASN ** F 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 GLN F 541 ASN F 548 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.110184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082705 restraints weight = 56743.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085766 restraints weight = 30784.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.086607 restraints weight = 18818.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.087083 restraints weight = 16463.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087260 restraints weight = 14955.356| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1774 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= 0.105 Angle : 0.516 11.525 35595 Z= 0.263 Chirality : 0.041 0.167 3984 Planarity : 0.004 0.055 4537 Dihedral : 9.134 157.833 3667 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.09 % Favored : 95.85 % Rotamer: Outliers : 2.50 % Allowed : 17.20 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.15), residues: 3133 helix: 0.65 (0.16), residues: 1153 sheet: -1.09 (0.25), residues: 481 loop : -1.28 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 99 TYR 0.016 0.001 TYR B 482 PHE 0.009 0.001 PHE D 626 TRP 0.009 0.001 TRP A 350 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00245 (26281) covalent geometry : angle 0.51575 (35593) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.61431 ( 2) hydrogen bonds : bond 0.02990 ( 836) hydrogen bonds : angle 4.23062 ( 2358) *********************** 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 284 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7440 (ttp80) REVERT: A 534 ASP cc_start: 0.8040 (t70) cc_final: 0.7691 (t70) REVERT: C 382 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7813 (mm-30) REVERT: C 471 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9267 (pp) REVERT: D 522 ASP cc_start: 0.8457 (t70) cc_final: 0.8110 (t0) REVERT: D 660 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: E 382 GLU cc_start: 0.7543 (mp0) cc_final: 0.7054 (mp0) REVERT: E 426 MET cc_start: 0.7225 (mmm) cc_final: 0.6977 (mmm) REVERT: E 560 ASP cc_start: 0.7344 (t0) cc_final: 0.6561 (m-30) REVERT: E 660 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: F 332 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8152 (ttm-80) REVERT: F 547 MET cc_start: 0.8502 (ttm) cc_final: 0.8228 (ttm) REVERT: F 684 MET cc_start: 0.8085 (tpp) cc_final: 0.7586 (tpp) outliers start: 72 outliers final: 57 residues processed: 268 average time/residue: 0.1558 time to fit residues: 67.4436 Evaluate side-chains 254 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 194 ILE 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 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 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL 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 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 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 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 624 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 660 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 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 332 ARG Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 511 THR Chi-restraints excluded: chain F residue 532 LEU 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 135 ILE Chi-restraints excluded: chain K residue 183 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 164 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 106 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 193 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 281 optimal weight: 0.3980 chunk 207 optimal weight: 0.0050 chunk 268 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082290 restraints weight = 56542.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085526 restraints weight = 30541.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086232 restraints weight = 18621.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086656 restraints weight = 16592.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.086778 restraints weight = 15079.975| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26282 Z= 0.121 Angle : 0.522 11.116 35595 Z= 0.266 Chirality : 0.041 0.187 3984 Planarity : 0.004 0.055 4537 Dihedral : 9.048 157.791 3667 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.20 % Rotamer: Outliers : 2.81 % Allowed : 17.34 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.15), residues: 3133 helix: 0.80 (0.16), residues: 1135 sheet: -1.08 (0.25), residues: 483 loop : -1.25 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 99 TYR 0.017 0.001 TYR C 482 PHE 0.010 0.001 PHE A 243 TRP 0.010 0.001 TRP A 350 HIS 0.002 0.001 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00286 (26281) covalent geometry : angle 0.52151 (35593) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.61744 ( 2) hydrogen bonds : bond 0.03068 ( 836) hydrogen bonds : angle 4.20020 ( 2358) *********************** 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 290 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8087 (t70) cc_final: 0.7738 (t70) REVERT: B 522 ASP cc_start: 0.8298 (m-30) cc_final: 0.8025 (m-30) REVERT: B 572 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: C 382 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 471 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9281 (pp) REVERT: D 367 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9003 (tp) REVERT: D 522 ASP cc_start: 0.8460 (t70) cc_final: 0.8111 (t0) REVERT: D 660 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: E 382 GLU cc_start: 0.7534 (mp0) cc_final: 0.7040 (mp0) REVERT: E 426 MET cc_start: 0.7298 (mmm) cc_final: 0.7039 (mmm) REVERT: E 560 ASP cc_start: 0.7412 (t0) cc_final: 0.6607 (m-30) REVERT: E 561 PHE cc_start: 0.5601 (m-10) cc_final: 0.5011 (m-10) REVERT: E 660 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: F 180 LEU cc_start: 0.7955 (tt) cc_final: 0.7378 (mt) REVERT: F 332 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8051 (ttm-80) REVERT: F 547 MET cc_start: 0.8524 (ttm) cc_final: 0.8226 (ttm) REVERT: F 684 MET cc_start: 0.8233 (tpp) cc_final: 0.7886 (tpp) outliers start: 81 outliers final: 60 residues processed: 272 average time/residue: 0.1556 time to fit residues: 68.0395 Evaluate side-chains 263 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 197 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 194 ILE 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 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 413 LEU Chi-restraints excluded: chain A residue 505 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 486 LEU Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL 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 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 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 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 E residue 383 LEU 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 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 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 532 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 257 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 284 optimal weight: 0.0980 chunk 159 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 287 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 43 optimal weight: 0.0370 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN F 548 HIS ** 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 = 0.3579 r_free = 0.3579 target = 0.112024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083356 restraints weight = 56377.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086004 restraints weight = 30528.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087737 restraints weight = 20756.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088835 restraints weight = 16269.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089536 restraints weight = 13971.516| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26282 Z= 0.093 Angle : 0.509 12.211 35595 Z= 0.259 Chirality : 0.041 0.164 3984 Planarity : 0.003 0.055 4537 Dihedral : 8.744 157.405 3667 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 2.32 % Allowed : 17.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3133 helix: 0.94 (0.16), residues: 1135 sheet: -0.99 (0.25), residues: 493 loop : -1.15 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 99 TYR 0.014 0.001 TYR B 482 PHE 0.010 0.001 PHE A 243 TRP 0.008 0.000 TRP A 350 HIS 0.004 0.000 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00211 (26281) covalent geometry : angle 0.50945 (35593) SS BOND : bond 0.00013 ( 1) SS BOND : angle 0.47662 ( 2) hydrogen bonds : bond 0.02700 ( 836) hydrogen bonds : angle 4.01907 ( 2358) *********************** 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 289 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 222 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 ASP cc_start: 0.8047 (t70) cc_final: 0.7733 (t70) REVERT: B 522 ASP cc_start: 0.8313 (m-30) cc_final: 0.8023 (m-30) REVERT: C 382 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 471 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9269 (pp) REVERT: D 367 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8895 (tp) REVERT: D 522 ASP cc_start: 0.8427 (t70) cc_final: 0.8085 (t0) REVERT: D 660 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: E 382 GLU cc_start: 0.7553 (mp0) cc_final: 0.7021 (mp0) REVERT: E 426 MET cc_start: 0.7274 (mmm) cc_final: 0.7006 (mmm) REVERT: E 560 ASP cc_start: 0.7188 (t0) cc_final: 0.6362 (m-30) REVERT: E 561 PHE cc_start: 0.5457 (m-10) cc_final: 0.4893 (m-10) REVERT: E 660 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8387 (mp10) REVERT: E 684 MET cc_start: 0.8336 (tmm) cc_final: 0.7845 (tmm) REVERT: F 180 LEU cc_start: 0.8026 (tt) cc_final: 0.7470 (mt) REVERT: F 332 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8274 (ttm-80) REVERT: F 399 MET cc_start: 0.8538 (mtt) cc_final: 0.8257 (mtt) REVERT: F 547 MET cc_start: 0.8516 (ttm) cc_final: 0.8238 (ttm) REVERT: F 684 MET cc_start: 0.8292 (tpp) cc_final: 0.8037 (tpp) outliers start: 67 outliers final: 51 residues processed: 273 average time/residue: 0.1539 time to fit residues: 66.7851 Evaluate side-chains 266 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 194 ILE 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 365 THR 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 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 624 VAL 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 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 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 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 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 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 532 LEU 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 183 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 55 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 259 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 190 optimal weight: 0.5980 chunk 291 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 201 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.108549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.081050 restraints weight = 57016.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.084026 restraints weight = 31001.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085000 restraints weight = 19266.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085414 restraints weight = 16352.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085589 restraints weight = 15337.759| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2086 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= 0.173 Angle : 0.576 12.847 35595 Z= 0.293 Chirality : 0.043 0.242 3984 Planarity : 0.004 0.055 4537 Dihedral : 8.877 158.583 3667 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.56 % Favored : 95.37 % Rotamer: Outliers : 2.53 % Allowed : 18.11 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.15), residues: 3133 helix: 0.89 (0.16), residues: 1117 sheet: -1.09 (0.24), residues: 495 loop : -1.15 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 99 TYR 0.023 0.001 TYR A 482 PHE 0.033 0.001 PHE A 120 TRP 0.012 0.001 TRP A 350 HIS 0.003 0.001 HIS F 312 Details of bonding type rmsd covalent geometry : bond 0.00412 (26281) covalent geometry : angle 0.57563 (35593) SS BOND : bond 0.00353 ( 1) SS BOND : angle 0.79766 ( 2) hydrogen bonds : bond 0.03586 ( 836) hydrogen bonds : angle 4.25946 ( 2358) *********************** 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 279 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 206 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7612 (ttp80) REVERT: A 534 ASP cc_start: 0.8127 (t70) cc_final: 0.7765 (t70) REVERT: B 572 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: C 382 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7820 (mm-30) REVERT: C 471 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9292 (pp) REVERT: D 522 ASP cc_start: 0.8461 (t70) cc_final: 0.8119 (t0) REVERT: D 660 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: E 382 GLU cc_start: 0.7573 (mp0) cc_final: 0.7035 (mp0) REVERT: E 426 MET cc_start: 0.7360 (mmm) cc_final: 0.7089 (mmm) REVERT: E 560 ASP cc_start: 0.7303 (t0) cc_final: 0.6508 (m-30) REVERT: E 561 PHE cc_start: 0.5635 (m-10) cc_final: 0.5036 (m-10) REVERT: E 660 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: F 288 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8567 (mmm160) REVERT: F 399 MET cc_start: 0.8575 (mtt) cc_final: 0.8333 (mtt) REVERT: F 684 MET cc_start: 0.8374 (tpp) cc_final: 0.8165 (tpp) outliers start: 73 outliers final: 58 residues processed: 266 average time/residue: 0.1692 time to fit residues: 72.1700 Evaluate side-chains 257 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 194 ILE 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 346 ASP 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 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 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 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 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 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 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 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 183 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 128 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 1 optimal weight: 0.0770 chunk 274 optimal weight: 0.3980 chunk 252 optimal weight: 0.7980 chunk 197 optimal weight: 2.9990 chunk 223 optimal weight: 9.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082050 restraints weight = 56526.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085424 restraints weight = 30293.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086170 restraints weight = 18090.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086535 restraints weight = 16177.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086640 restraints weight = 14683.126| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26282 Z= 0.126 Angle : 0.553 13.210 35595 Z= 0.279 Chirality : 0.042 0.244 3984 Planarity : 0.004 0.060 4537 Dihedral : 8.725 157.786 3667 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.29 % Allowed : 18.31 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.15), residues: 3133 helix: 0.87 (0.16), residues: 1135 sheet: -1.07 (0.24), residues: 495 loop : -1.12 (0.16), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 152 TYR 0.017 0.001 TYR A 482 PHE 0.031 0.001 PHE A 120 TRP 0.010 0.001 TRP A 350 HIS 0.003 0.001 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00299 (26281) covalent geometry : angle 0.55317 (35593) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.54173 ( 2) hydrogen bonds : bond 0.03059 ( 836) hydrogen bonds : angle 4.12408 ( 2358) ********************** 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 270 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7603 (ttp80) REVERT: A 534 ASP cc_start: 0.8112 (t70) cc_final: 0.7734 (t70) REVERT: B 572 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: C 382 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7854 (mm-30) REVERT: C 471 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9279 (pp) REVERT: D 367 LEU cc_start: 0.9280 (tt) cc_final: 0.8972 (tp) REVERT: D 522 ASP cc_start: 0.8460 (t70) cc_final: 0.8076 (t0) REVERT: D 660 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: E 382 GLU cc_start: 0.7560 (mp0) cc_final: 0.7019 (mp0) REVERT: E 426 MET cc_start: 0.7323 (mmm) cc_final: 0.7055 (mmm) REVERT: E 560 ASP cc_start: 0.7353 (t0) cc_final: 0.6551 (m-30) REVERT: E 561 PHE cc_start: 0.5605 (m-10) cc_final: 0.5028 (m-10) REVERT: E 660 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: E 684 MET cc_start: 0.8435 (tmm) cc_final: 0.7945 (tmm) REVERT: F 288 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8547 (mmm160) outliers start: 66 outliers final: 57 residues processed: 256 average time/residue: 0.1758 time to fit residues: 71.5641 Evaluate side-chains 256 residues out of total 2883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 194 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 194 ILE 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 365 THR 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 497 CYS Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 491 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 684 MET 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 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 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 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 582 VAL Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 183 VAL 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 160 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 295 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 172 optimal weight: 8.9990 chunk 170 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 278 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081506 restraints weight = 56075.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084047 restraints weight = 30860.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085723 restraints weight = 21216.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086795 restraints weight = 16707.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087457 restraints weight = 14392.983| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26282 Z= 0.126 Angle : 0.558 13.155 35595 Z= 0.281 Chirality : 0.042 0.240 3984 Planarity : 0.004 0.055 4537 Dihedral : 8.675 158.335 3667 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 2.32 % Allowed : 18.49 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3133 helix: 0.96 (0.16), residues: 1117 sheet: -1.07 (0.24), residues: 495 loop : -1.08 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 152 TYR 0.017 0.001 TYR A 482 PHE 0.033 0.001 PHE A 120 TRP 0.010 0.001 TRP A 350 HIS 0.002 0.001 HIS K 109 Details of bonding type rmsd covalent geometry : bond 0.00299 (26281) covalent geometry : angle 0.55787 (35593) SS BOND : bond 0.00178 ( 1) SS BOND : angle 0.57428 ( 2) hydrogen bonds : bond 0.03144 ( 836) hydrogen bonds : angle 4.12142 ( 2358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.45 seconds wall clock time: 62 minutes 58.51 seconds (3778.51 seconds total)