Starting phenix.real_space_refine on Thu Feb 5 13:38:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j63_61161/02_2026/9j63_61161.map" } resolution = 3.93 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3696 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 6 6.06 5 S 115 5.16 5 C 9258 2.51 5 N 2445 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14518 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5213 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "B" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain breaks: 2 Chain: "E" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 601 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain breaks: 1 Chain: "D" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5213 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "G" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 734 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 7, 'TRANS': 84} Chain breaks: 2 Chain: "H" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain breaks: 1 Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6818 SG CYS E 42 81.503 75.332 107.460 1.00 50.88 S ATOM 6837 SG CYS E 45 80.984 75.737 110.967 1.00 49.07 S ATOM 7063 SG CYS E 83 80.483 78.989 109.395 1.00 50.97 S ATOM 6992 SG CYS E 75 82.035 75.750 95.018 1.00 53.50 S ATOM 7159 SG CYS E 94 84.116 76.663 97.604 1.00 41.16 S ATOM 6904 SG CYS E 53 77.031 80.486 112.772 1.00 52.95 S ATOM 6927 SG CYS E 56 73.889 82.062 113.940 1.00 51.59 S ATOM 6942 SG CYS E 68 73.818 79.351 111.339 1.00 67.21 S ATOM 14080 SG CYS H 42 90.543 60.963 108.741 1.00 70.61 S ATOM 14099 SG CYS H 45 90.838 59.432 112.050 1.00 60.48 S ATOM 14230 SG CYS H 75 87.041 61.539 95.689 1.00 63.95 S ATOM 14397 SG CYS H 94 86.603 58.704 97.492 1.00 51.52 S ATOM 14166 SG CYS H 53 93.315 54.066 114.000 1.00 69.45 S ATOM 14180 SG CYS H 68 96.574 53.810 112.251 1.00 72.13 S Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14518 At special positions: 0 Unit cell: (170.15, 136.12, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 6 29.99 S 115 16.00 O 2694 8.00 N 2445 7.00 C 9258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 422.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" ND1 HIS E 80 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 45 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 83 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 42 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 94 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 75 " pdb=" ZN E 203 " pdb="ZN ZN E 203 " - pdb=" ND1 HIS E 82 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 68 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 53 " pdb="ZN ZN E 203 " - pdb=" SG CYS E 56 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 42 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 45 " pdb="ZN ZN H 201 " - pdb=" ND1 HIS H 80 " pdb=" ZN H 202 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 94 " pdb="ZN ZN H 202 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 202 " - pdb=" SG CYS H 75 " pdb=" ZN H 203 " pdb="ZN ZN H 203 " - pdb=" ND1 HIS H 82 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 68 " pdb="ZN ZN H 203 " - pdb=" SG CYS H 53 " Number of angles added : 6 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 62.7% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 removed outlier: 3.627A pdb=" N THR A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 47 Processing helix chain 'A' and resid 53 through 79 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 105 through 112 Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 138 through 151 Processing helix chain 'A' and resid 155 through 172 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.731A pdb=" N ILE A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 207 through 230 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 271 removed outlier: 3.656A pdb=" N MET A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.656A pdb=" N CYS A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 286 " --> pdb=" O CYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.185A pdb=" N VAL A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 4.320A pdb=" N HIS A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 358 removed outlier: 3.523A pdb=" N VAL A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 377 removed outlier: 3.586A pdb=" N ALA A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 removed outlier: 4.576A pdb=" N GLU A 389 " --> pdb=" O CYS A 385 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N CYS A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.842A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 445 removed outlier: 3.528A pdb=" N PHE A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 470 removed outlier: 3.698A pdb=" N MET A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N TYR A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N GLU A 468 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 469 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 497 removed outlier: 3.827A pdb=" N MET A 480 " --> pdb=" O MET A 476 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 481 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASP A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 494 " --> pdb=" O PHE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 548 removed outlier: 4.718A pdb=" N SER A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 579 through 587 removed outlier: 3.625A pdb=" N ALA A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 584 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 585 " --> pdb=" O GLN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 604 Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'C' and resid 66 through 84 Processing helix chain 'C' and resid 96 through 111 removed outlier: 4.694A pdb=" N LEU C 101 " --> pdb=" O PRO C 97 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.535A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'E' and resid 81 through 91 Processing helix chain 'D' and resid 9 through 26 removed outlier: 3.599A pdb=" N THR D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 53 through 79 Processing helix chain 'D' and resid 82 through 105 removed outlier: 3.672A pdb=" N LYS D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 112 Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 155 through 172 Processing helix chain 'D' and resid 177 through 192 removed outlier: 3.579A pdb=" N ILE D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLU D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 207 through 230 Processing helix chain 'D' and resid 231 through 254 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 271 removed outlier: 3.644A pdb=" N MET D 270 " --> pdb=" O CYS D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 286 removed outlier: 4.244A pdb=" N HIS D 283 " --> pdb=" O HIS D 279 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASN D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 286 " --> pdb=" O CYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 4.241A pdb=" N VAL D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 327 removed outlier: 4.371A pdb=" N HIS D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET D 311 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 358 Processing helix chain 'D' and resid 361 through 377 removed outlier: 3.579A pdb=" N ALA D 371 " --> pdb=" O ALA D 367 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 removed outlier: 4.650A pdb=" N GLU D 389 " --> pdb=" O CYS D 385 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N CYS D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 423 removed outlier: 3.659A pdb=" N ASP D 413 " --> pdb=" O ASN D 409 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR D 420 " --> pdb=" O THR D 416 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL D 421 " --> pdb=" O SER D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 445 Processing helix chain 'D' and resid 450 through 470 removed outlier: 3.549A pdb=" N MET D 457 " --> pdb=" O SER D 453 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N TYR D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N GLU D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE D 469 " --> pdb=" O CYS D 465 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 470 " --> pdb=" O GLY D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 497 removed outlier: 3.888A pdb=" N MET D 480 " --> pdb=" O MET D 476 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER D 481 " --> pdb=" O TYR D 477 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE D 493 " --> pdb=" O LYS D 489 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 494 " --> pdb=" O PHE D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 548 removed outlier: 3.548A pdb=" N LYS D 535 " --> pdb=" O GLN D 531 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER D 536 " --> pdb=" O GLU D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 559 No H-bonds generated for 'chain 'D' and resid 557 through 559' Processing helix chain 'D' and resid 579 through 587 removed outlier: 3.623A pdb=" N ALA D 587 " --> pdb=" O ALA D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 604 Processing helix chain 'D' and resid 606 through 620 Processing helix chain 'F' and resid 33 through 39 removed outlier: 3.992A pdb=" N SER F 39 " --> pdb=" O HIS F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 66 through 84 Processing helix chain 'F' and resid 96 through 111 removed outlier: 4.697A pdb=" N LEU F 101 " --> pdb=" O PRO F 97 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 35 removed outlier: 3.886A pdb=" N LEU G 27 " --> pdb=" O THR G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'H' and resid 80 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.061A pdb=" N SER A 506 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN A 508 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA E 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR A 510 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TRP E 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 506 through 513 removed outlier: 6.061A pdb=" N SER A 506 " --> pdb=" O TRP E 27 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA E 29 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLN A 508 " --> pdb=" O ALA E 29 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA E 31 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR A 510 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TRP E 33 " --> pdb=" O TYR A 510 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 512 " --> pdb=" O TRP E 33 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A 575 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR A 573 " --> pdb=" O MET A 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 593 through 594 Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 61 removed outlier: 5.177A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 10.783A pdb=" N ASP B 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AA6, first strand: chain 'E' and resid 78 through 80 Processing sheet with id=AA7, first strand: chain 'D' and resid 506 through 513 removed outlier: 6.103A pdb=" N SER D 506 " --> pdb=" O TRP H 27 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA H 29 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN D 508 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA H 31 " --> pdb=" O GLN D 508 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR D 510 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TRP H 33 " --> pdb=" O TYR D 510 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 512 " --> pdb=" O TRP H 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 506 through 513 removed outlier: 6.103A pdb=" N SER D 506 " --> pdb=" O TRP H 27 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA H 29 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN D 508 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ALA H 31 " --> pdb=" O GLN D 508 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR D 510 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N TRP H 33 " --> pdb=" O TYR D 510 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 512 " --> pdb=" O TRP H 33 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 564 " --> pdb=" O ALA D 575 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 575 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET D 566 " --> pdb=" O TYR D 573 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D 573 " --> pdb=" O MET D 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 593 through 595 Processing sheet with id=AB1, first strand: chain 'F' and resid 58 through 61 removed outlier: 7.481A pdb=" N TYR F 18 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N VAL F 60 " --> pdb=" O TYR F 18 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS F 20 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LYS F 32 " --> pdb=" O PHE G 15 " (cutoff:3.500A) removed outlier: 10.932A pdb=" N ASP G 17 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N ALA G 73 " --> pdb=" O ASP G 2 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE G 4 " --> pdb=" O ALA G 73 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N VAL G 75 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET G 6 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 77 " --> pdb=" O MET G 6 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG G 8 " --> pdb=" O LEU G 77 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2406 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: 2.35 Time building geometry restraints manager: 1.93 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: 2951 1.33 - 1.45: 3423 1.45 - 1.57: 8258 1.57 - 1.69: 0 1.69 - 1.82: 187 Bond restraints: 14819 Sorted by residual: bond pdb=" N VAL E 93 " pdb=" CA VAL E 93 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.11e-02 8.12e+03 1.09e+01 bond pdb=" N VAL D 7 " pdb=" CA VAL D 7 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.10e-02 8.26e+03 1.05e+01 bond pdb=" N CYS E 42 " pdb=" CA CYS E 42 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N TYR D 49 " pdb=" CA TYR D 49 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 1.01e+01 bond pdb=" N VAL A 7 " pdb=" CA VAL A 7 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.10e-02 8.26e+03 9.50e+00 ... (remaining 14814 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 18912 1.38 - 2.76: 843 2.76 - 4.14: 171 4.14 - 5.52: 52 5.52 - 6.89: 12 Bond angle restraints: 19990 Sorted by residual: angle pdb=" C HIS B 10 " pdb=" CA HIS B 10 " pdb=" CB HIS B 10 " ideal model delta sigma weight residual 117.23 111.17 6.06 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N VAL C 73 " pdb=" CA VAL C 73 " pdb=" C VAL C 73 " ideal model delta sigma weight residual 110.72 106.59 4.13 1.01e+00 9.80e-01 1.67e+01 angle pdb=" C TYR A 219 " pdb=" CA TYR A 219 " pdb=" CB TYR A 219 " ideal model delta sigma weight residual 110.85 117.74 -6.89 1.70e+00 3.46e-01 1.64e+01 angle pdb=" N ASN E 98 " pdb=" CA ASN E 98 " pdb=" C ASN E 98 " ideal model delta sigma weight residual 112.24 107.11 5.13 1.28e+00 6.10e-01 1.61e+01 angle pdb=" CA PHE A 10 " pdb=" C PHE A 10 " pdb=" O PHE A 10 " ideal model delta sigma weight residual 120.42 116.18 4.24 1.06e+00 8.90e-01 1.60e+01 ... (remaining 19985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8252 17.90 - 35.80: 632 35.80 - 53.71: 89 53.71 - 71.61: 12 71.61 - 89.51: 9 Dihedral angle restraints: 8994 sinusoidal: 3721 harmonic: 5273 Sorted by residual: dihedral pdb=" C TYR A 219 " pdb=" N TYR A 219 " pdb=" CA TYR A 219 " pdb=" CB TYR A 219 " ideal model delta harmonic sigma weight residual -122.60 -133.63 11.03 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" CA ARG B 29 " pdb=" C ARG B 29 " pdb=" N ILE B 30 " pdb=" CA ILE B 30 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA MET A 406 " pdb=" C MET A 406 " pdb=" N THR A 407 " pdb=" CA THR A 407 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 8991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1908 0.064 - 0.129: 252 0.129 - 0.193: 34 0.193 - 0.258: 6 0.258 - 0.322: 2 Chirality restraints: 2202 Sorted by residual: chirality pdb=" CA TYR A 219 " pdb=" N TYR A 219 " pdb=" C TYR A 219 " pdb=" CB TYR A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ASP H 97 " pdb=" N ASP H 97 " pdb=" C ASP H 97 " pdb=" CB ASP H 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA GLN E 104 " pdb=" N GLN E 104 " pdb=" C GLN E 104 " pdb=" CB GLN E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2199 not shown) Planarity restraints: 2539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 52 " 0.019 2.00e-02 2.50e+03 3.75e-02 1.40e+01 pdb=" C LEU E 52 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU E 52 " 0.025 2.00e-02 2.50e+03 pdb=" N CYS E 53 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 10 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C PHE A 10 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 10 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 11 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 77 " 0.015 2.00e-02 2.50e+03 1.53e-02 4.10e+00 pdb=" CG PHE F 77 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 77 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE F 77 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 77 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 77 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE F 77 " 0.001 2.00e-02 2.50e+03 ... (remaining 2536 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1338 2.74 - 3.28: 15650 3.28 - 3.82: 25233 3.82 - 4.36: 29897 4.36 - 4.90: 48128 Nonbonded interactions: 120246 Sorted by model distance: nonbonded pdb=" O LEU D 324 " pdb=" OG SER D 328 " model vdw 2.202 3.040 nonbonded pdb=" O LEU A 324 " pdb=" OG SER A 328 " model vdw 2.203 3.040 nonbonded pdb=" O CYS H 42 " pdb=" NH2 ARG H 46 " model vdw 2.215 3.120 nonbonded pdb=" OG SER C 23 " pdb=" OD1 ASP C 25 " model vdw 2.238 3.040 nonbonded pdb=" OG SER F 39 " pdb=" O LEU F 110 " model vdw 2.240 3.040 ... (remaining 120241 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' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'E' and (resid 24 through 54 or resid 68 through 203)) selection = (chain 'H' and (resid 24 through 105 or resid 201 through 203)) } 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.230 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 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 : 0.005 0.236 14839 Z= 0.318 Angle : 0.721 18.092 19996 Z= 0.452 Chirality : 0.047 0.322 2202 Planarity : 0.003 0.039 2539 Dihedral : 12.783 89.511 5554 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.56 % Allowed : 0.87 % Favored : 98.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.21), residues: 1738 helix: 1.45 (0.17), residues: 1027 sheet: -0.29 (0.51), residues: 96 loop : 0.12 (0.26), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 33 TYR 0.018 0.001 TYR D 90 PHE 0.035 0.001 PHE F 77 TRP 0.014 0.002 TRP A 91 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00447 (14819) covalent geometry : angle 0.69386 (19990) hydrogen bonds : bond 0.20832 ( 816) hydrogen bonds : angle 7.10949 ( 2406) metal coordination : bond 0.08606 ( 20) metal coordination : angle 11.24889 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 463 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.8029 (mm) cc_final: 0.7796 (mm) REVERT: A 309 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8643 (Cg_endo) REVERT: A 406 MET cc_start: 0.6462 (ppp) cc_final: 0.6128 (pmm) REVERT: A 407 THR cc_start: 0.6080 (m) cc_final: 0.5867 (m) REVERT: A 438 MET cc_start: 0.7446 (tmm) cc_final: 0.6894 (mmt) REVERT: A 457 MET cc_start: 0.8435 (tpp) cc_final: 0.8114 (tpt) REVERT: A 561 THR cc_start: 0.8701 (p) cc_final: 0.8446 (p) REVERT: A 638 PHE cc_start: 0.6731 (m-80) cc_final: 0.6456 (m-80) REVERT: C 43 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8595 (mttt) REVERT: C 58 ASN cc_start: 0.5846 (m-40) cc_final: 0.5111 (p0) REVERT: C 105 MET cc_start: 0.5872 (ptt) cc_final: 0.5255 (mmt) REVERT: D 35 TRP cc_start: 0.5960 (t-100) cc_final: 0.5584 (t-100) REVERT: D 62 LYS cc_start: 0.7332 (tttt) cc_final: 0.6974 (tmtt) REVERT: D 107 TYR cc_start: 0.6181 (t80) cc_final: 0.5094 (t80) REVERT: D 477 TYR cc_start: 0.8158 (t80) cc_final: 0.7641 (t80) REVERT: D 509 ILE cc_start: 0.8925 (tt) cc_final: 0.8461 (tt) REVERT: D 561 THR cc_start: 0.8840 (p) cc_final: 0.8525 (p) REVERT: F 35 HIS cc_start: 0.5763 (m90) cc_final: 0.4919 (t-170) REVERT: F 43 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8321 (mttt) REVERT: F 105 MET cc_start: 0.5920 (ptt) cc_final: 0.4485 (mmt) REVERT: H 98 ASN cc_start: 0.7370 (m110) cc_final: 0.6990 (t0) REVERT: H 99 ARG cc_start: 0.4590 (pmt-80) cc_final: 0.4282 (ttp-170) outliers start: 9 outliers final: 2 residues processed: 467 average time/residue: 0.1361 time to fit residues: 90.7837 Evaluate side-chains 284 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 282 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 71 HIS A 73 HIS A 221 GLN A 225 ASN A 228 GLN A 283 HIS ** A 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 GLN A 624 ASN C 108 ASN D 15 ASN D 68 HIS D 73 HIS D 228 GLN D 279 HIS D 283 HIS D 288 GLN D 513 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.215923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.184824 restraints weight = 26114.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.187244 restraints weight = 46596.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.187570 restraints weight = 26996.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.187789 restraints weight = 20764.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.188957 restraints weight = 16707.243| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14839 Z= 0.171 Angle : 0.679 14.869 19996 Z= 0.357 Chirality : 0.041 0.181 2202 Planarity : 0.006 0.188 2539 Dihedral : 4.863 59.686 1919 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.72 % Allowed : 11.39 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 1738 helix: 1.32 (0.16), residues: 1034 sheet: 0.26 (0.46), residues: 124 loop : -0.01 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 251 TYR 0.020 0.002 TYR A 378 PHE 0.030 0.002 PHE A 39 TRP 0.023 0.002 TRP A 35 HIS 0.015 0.001 HIS E 77 Details of bonding type rmsd covalent geometry : bond 0.00364 (14819) covalent geometry : angle 0.67005 (19990) hydrogen bonds : bond 0.05994 ( 816) hydrogen bonds : angle 5.47839 ( 2406) metal coordination : bond 0.01331 ( 20) metal coordination : angle 6.52675 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 312 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 TYR cc_start: 0.6850 (t80) cc_final: 0.6179 (t80) REVERT: A 259 TYR cc_start: 0.6163 (m-10) cc_final: 0.5943 (m-80) REVERT: A 270 MET cc_start: 0.7298 (tmm) cc_final: 0.7083 (tmm) REVERT: A 457 MET cc_start: 0.8407 (tpp) cc_final: 0.8186 (tpp) REVERT: A 561 THR cc_start: 0.8815 (p) cc_final: 0.8597 (p) REVERT: C 105 MET cc_start: 0.5331 (ptt) cc_final: 0.4835 (mmt) REVERT: B 5 LEU cc_start: 0.6886 (mm) cc_final: 0.6583 (tp) REVERT: B 22 SER cc_start: 0.7084 (m) cc_final: 0.6763 (m) REVERT: E 89 LYS cc_start: 0.7936 (mtmm) cc_final: 0.7731 (mtmm) REVERT: D 62 LYS cc_start: 0.7180 (tttt) cc_final: 0.6979 (tmtt) REVERT: D 476 MET cc_start: 0.8232 (tpp) cc_final: 0.7272 (tpp) REVERT: D 539 MET cc_start: 0.7203 (tpp) cc_final: 0.6717 (tpp) REVERT: D 561 THR cc_start: 0.8741 (p) cc_final: 0.8483 (p) REVERT: F 43 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8375 (mttt) REVERT: F 75 MET cc_start: 0.4411 (ptt) cc_final: 0.4154 (ptt) REVERT: F 105 MET cc_start: 0.4441 (ptt) cc_final: 0.3879 (mmt) REVERT: H 27 TRP cc_start: 0.6693 (t60) cc_final: 0.6490 (t60) REVERT: H 98 ASN cc_start: 0.7777 (m110) cc_final: 0.7347 (t0) outliers start: 44 outliers final: 25 residues processed: 339 average time/residue: 0.1331 time to fit residues: 64.2024 Evaluate side-chains 279 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 352 GLN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain H residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 72 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 3 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN A 557 HIS B 10 HIS D 88 HIS D 274 HIS D 538 GLN D 547 HIS F 58 ASN ** H 77 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 = 0.4645 r_free = 0.4645 target = 0.208006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.174433 restraints weight = 25913.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.170607 restraints weight = 44846.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.170030 restraints weight = 28714.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168273 restraints weight = 30601.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.168617 restraints weight = 23929.959| |-----------------------------------------------------------------------------| r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14839 Z= 0.198 Angle : 0.681 14.450 19996 Z= 0.355 Chirality : 0.043 0.205 2202 Planarity : 0.004 0.084 2539 Dihedral : 4.396 18.741 1913 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.22 % Allowed : 13.80 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.20), residues: 1738 helix: 1.09 (0.16), residues: 1040 sheet: 0.27 (0.46), residues: 124 loop : -0.30 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 33 TYR 0.028 0.002 TYR A 43 PHE 0.037 0.003 PHE D 39 TRP 0.022 0.002 TRP D 14 HIS 0.008 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00439 (14819) covalent geometry : angle 0.67237 (19990) hydrogen bonds : bond 0.05410 ( 816) hydrogen bonds : angle 5.22753 ( 2406) metal coordination : bond 0.01235 ( 20) metal coordination : angle 6.11283 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7206 (mpp) cc_final: 0.6980 (mmm) REVERT: A 325 ARG cc_start: 0.7176 (mtm110) cc_final: 0.6820 (ttm-80) REVERT: A 582 MET cc_start: 0.6775 (ttm) cc_final: 0.6292 (ttt) REVERT: C 105 MET cc_start: 0.5748 (ptt) cc_final: 0.5177 (mmt) REVERT: B 22 SER cc_start: 0.7133 (m) cc_final: 0.6763 (m) REVERT: E 89 LYS cc_start: 0.8010 (mtmm) cc_final: 0.7692 (mtmm) REVERT: D 62 LYS cc_start: 0.7434 (tttt) cc_final: 0.7146 (tmtt) REVERT: D 476 MET cc_start: 0.8544 (tpp) cc_final: 0.8039 (tpp) REVERT: F 43 LYS cc_start: 0.8858 (mtmm) cc_final: 0.8363 (mttm) REVERT: F 75 MET cc_start: 0.4454 (ptt) cc_final: 0.4205 (ptt) REVERT: F 105 MET cc_start: 0.4958 (ptt) cc_final: 0.4078 (mmt) REVERT: H 98 ASN cc_start: 0.8054 (m110) cc_final: 0.7567 (t0) outliers start: 52 outliers final: 37 residues processed: 298 average time/residue: 0.1275 time to fit residues: 55.4700 Evaluate side-chains 266 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 492 ASN Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 250 CYS Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain F residue 95 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 74 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 126 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 chunk 17 optimal weight: 0.0670 chunk 26 optimal weight: 0.6980 chunk 93 optimal weight: 0.0870 chunk 168 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.205400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.173962 restraints weight = 26134.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.168254 restraints weight = 42897.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.166626 restraints weight = 33260.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.167377 restraints weight = 32067.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.167238 restraints weight = 24613.718| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14839 Z= 0.143 Angle : 0.620 11.286 19996 Z= 0.324 Chirality : 0.040 0.213 2202 Planarity : 0.004 0.043 2539 Dihedral : 4.327 21.581 1913 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.72 % Allowed : 15.53 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1738 helix: 1.09 (0.16), residues: 1048 sheet: 0.29 (0.46), residues: 124 loop : -0.36 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 75 TYR 0.026 0.001 TYR D 107 PHE 0.047 0.002 PHE D 39 TRP 0.023 0.002 TRP A 35 HIS 0.014 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00303 (14819) covalent geometry : angle 0.61648 (19990) hydrogen bonds : bond 0.04837 ( 816) hydrogen bonds : angle 5.08084 ( 2406) metal coordination : bond 0.00781 ( 20) metal coordination : angle 3.64246 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 247 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 GLN cc_start: 0.6298 (mt0) cc_final: 0.6096 (mm110) REVERT: A 270 MET cc_start: 0.7512 (tmm) cc_final: 0.7224 (tmm) REVERT: A 325 ARG cc_start: 0.7312 (mtm110) cc_final: 0.6925 (ttm-80) REVERT: A 457 MET cc_start: 0.8348 (tpp) cc_final: 0.7923 (tpp) REVERT: C 105 MET cc_start: 0.5519 (ptt) cc_final: 0.5116 (mmt) REVERT: B 22 SER cc_start: 0.7133 (m) cc_final: 0.6773 (m) REVERT: E 89 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7826 (mtmm) REVERT: D 62 LYS cc_start: 0.7369 (tttt) cc_final: 0.7143 (tmtt) REVERT: D 234 GLN cc_start: 0.6180 (mt0) cc_final: 0.5948 (mm-40) REVERT: D 476 MET cc_start: 0.8387 (tpp) cc_final: 0.6589 (mtt) REVERT: F 43 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8238 (mttm) REVERT: F 75 MET cc_start: 0.4458 (ptt) cc_final: 0.4223 (ptt) REVERT: F 105 MET cc_start: 0.4716 (ptt) cc_final: 0.4052 (mmt) REVERT: H 98 ASN cc_start: 0.8110 (m110) cc_final: 0.7601 (t0) outliers start: 44 outliers final: 32 residues processed: 275 average time/residue: 0.1315 time to fit residues: 52.5219 Evaluate side-chains 256 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 470 THR Chi-restraints excluded: chain D residue 582 MET Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 32 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 146 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS D 68 HIS ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.196880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160891 restraints weight = 25567.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156301 restraints weight = 44976.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.154471 restraints weight = 33321.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154626 restraints weight = 30024.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.153734 restraints weight = 26442.372| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14839 Z= 0.255 Angle : 0.735 13.493 19996 Z= 0.385 Chirality : 0.045 0.213 2202 Planarity : 0.004 0.051 2539 Dihedral : 4.538 24.774 1913 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.34 % Allowed : 16.65 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1738 helix: 0.91 (0.16), residues: 1032 sheet: 0.69 (0.52), residues: 94 loop : -0.47 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 89 TYR 0.025 0.002 TYR A 558 PHE 0.054 0.003 PHE D 39 TRP 0.030 0.003 TRP D 35 HIS 0.029 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00585 (14819) covalent geometry : angle 0.73272 (19990) hydrogen bonds : bond 0.05288 ( 816) hydrogen bonds : angle 5.19158 ( 2406) metal coordination : bond 0.00901 ( 20) metal coordination : angle 3.15540 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LEU cc_start: 0.7270 (tt) cc_final: 0.6995 (tt) REVERT: A 94 TYR cc_start: 0.8000 (t80) cc_final: 0.7682 (t80) REVERT: A 234 GLN cc_start: 0.6843 (mt0) cc_final: 0.6431 (mm-40) REVERT: A 457 MET cc_start: 0.8557 (tpp) cc_final: 0.8232 (tpp) REVERT: A 473 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 476 MET cc_start: 0.8886 (mmm) cc_final: 0.7989 (tpp) REVERT: C 32 LYS cc_start: 0.8658 (tppt) cc_final: 0.8267 (tppt) REVERT: C 105 MET cc_start: 0.5853 (ptt) cc_final: 0.5387 (mmt) REVERT: B 22 SER cc_start: 0.7307 (m) cc_final: 0.6878 (m) REVERT: E 89 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7920 (mtmm) REVERT: D 62 LYS cc_start: 0.7598 (tttt) cc_final: 0.7382 (tmtt) REVERT: D 234 GLN cc_start: 0.6621 (mt0) cc_final: 0.6294 (mm-40) REVERT: D 293 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6812 (t70) REVERT: D 476 MET cc_start: 0.8518 (tpp) cc_final: 0.7294 (mtt) REVERT: F 75 MET cc_start: 0.4616 (ptt) cc_final: 0.4384 (ptt) REVERT: F 105 MET cc_start: 0.5378 (ptt) cc_final: 0.4948 (mmt) REVERT: G 6 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.4586 (ppp) REVERT: H 98 ASN cc_start: 0.8210 (m110) cc_final: 0.7649 (t0) outliers start: 54 outliers final: 35 residues processed: 299 average time/residue: 0.1178 time to fit residues: 51.9424 Evaluate side-chains 268 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 32 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 157 optimal weight: 0.0030 chunk 162 optimal weight: 10.0000 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 ASN ** H 77 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 = 0.4508 r_free = 0.4508 target = 0.195270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.158939 restraints weight = 25419.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.154567 restraints weight = 44314.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.151537 restraints weight = 31865.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152390 restraints weight = 32177.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.152068 restraints weight = 22800.721| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.6099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14839 Z= 0.222 Angle : 0.703 10.425 19996 Z= 0.365 Chirality : 0.043 0.197 2202 Planarity : 0.004 0.050 2539 Dihedral : 4.595 22.860 1913 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.34 % Allowed : 18.38 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1738 helix: 0.87 (0.16), residues: 1038 sheet: 0.74 (0.51), residues: 94 loop : -0.55 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 33 TYR 0.028 0.002 TYR D 558 PHE 0.049 0.002 PHE D 39 TRP 0.028 0.002 TRP D 14 HIS 0.012 0.001 HIS H 77 Details of bonding type rmsd covalent geometry : bond 0.00518 (14819) covalent geometry : angle 0.70183 (19990) hydrogen bonds : bond 0.04964 ( 816) hydrogen bonds : angle 5.10338 ( 2406) metal coordination : bond 0.01341 ( 20) metal coordination : angle 2.80986 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 249 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8051 (t80) cc_final: 0.7799 (t80) REVERT: A 234 GLN cc_start: 0.6717 (mt0) cc_final: 0.6342 (mm-40) REVERT: A 270 MET cc_start: 0.7636 (tmm) cc_final: 0.7423 (tmm) REVERT: A 476 MET cc_start: 0.8899 (mmm) cc_final: 0.7026 (mtt) REVERT: A 544 TYR cc_start: 0.8154 (t80) cc_final: 0.7904 (t80) REVERT: C 32 LYS cc_start: 0.8319 (tppt) cc_final: 0.8088 (tppt) REVERT: C 105 MET cc_start: 0.5757 (ptt) cc_final: 0.5397 (mmt) REVERT: B 22 SER cc_start: 0.7097 (m) cc_final: 0.6692 (m) REVERT: E 89 LYS cc_start: 0.8305 (mtmm) cc_final: 0.7995 (mtmm) REVERT: D 234 GLN cc_start: 0.6544 (mt0) cc_final: 0.6266 (mm-40) REVERT: D 270 MET cc_start: 0.7694 (tmm) cc_final: 0.6896 (ttp) REVERT: D 293 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.6823 (t70) REVERT: D 476 MET cc_start: 0.8404 (tpp) cc_final: 0.7333 (mtt) REVERT: F 75 MET cc_start: 0.4634 (ptt) cc_final: 0.4404 (ptt) REVERT: F 105 MET cc_start: 0.5060 (ptt) cc_final: 0.4735 (mmt) REVERT: H 98 ASN cc_start: 0.8304 (m110) cc_final: 0.7627 (t0) outliers start: 54 outliers final: 44 residues processed: 294 average time/residue: 0.1197 time to fit residues: 51.5704 Evaluate side-chains 270 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 225 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS A 491 ASN D 88 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 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 = 0.4485 r_free = 0.4485 target = 0.193015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.154719 restraints weight = 25148.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.148675 restraints weight = 44887.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149797 restraints weight = 30024.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.147488 restraints weight = 30584.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.147628 restraints weight = 25775.039| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14839 Z= 0.257 Angle : 0.743 10.137 19996 Z= 0.388 Chirality : 0.044 0.149 2202 Planarity : 0.004 0.053 2539 Dihedral : 4.681 22.046 1913 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.71 % Allowed : 19.18 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.20), residues: 1738 helix: 0.74 (0.16), residues: 1036 sheet: 0.75 (0.51), residues: 94 loop : -0.58 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 33 TYR 0.021 0.002 TYR D 58 PHE 0.051 0.003 PHE A 39 TRP 0.027 0.003 TRP D 14 HIS 0.010 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00604 (14819) covalent geometry : angle 0.74151 (19990) hydrogen bonds : bond 0.05113 ( 816) hydrogen bonds : angle 5.23349 ( 2406) metal coordination : bond 0.01418 ( 20) metal coordination : angle 2.95258 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5377 (tmm) cc_final: 0.5079 (tmm) REVERT: A 94 TYR cc_start: 0.8160 (t80) cc_final: 0.7949 (t80) REVERT: A 234 GLN cc_start: 0.6835 (mt0) cc_final: 0.6388 (mm-40) REVERT: A 473 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8351 (mp) REVERT: C 32 LYS cc_start: 0.8597 (tppt) cc_final: 0.7806 (tppt) REVERT: C 33 ARG cc_start: 0.7876 (mmp80) cc_final: 0.7643 (mmp80) REVERT: C 105 MET cc_start: 0.6000 (ptt) cc_final: 0.5617 (mmt) REVERT: B 22 SER cc_start: 0.7102 (m) cc_final: 0.6653 (m) REVERT: E 89 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8198 (mtmm) REVERT: D 62 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7571 (tppt) REVERT: D 192 GLU cc_start: 0.7702 (pt0) cc_final: 0.7430 (pt0) REVERT: D 234 GLN cc_start: 0.6857 (mt0) cc_final: 0.6365 (mm-40) REVERT: D 293 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.6977 (t70) REVERT: D 476 MET cc_start: 0.8446 (tpp) cc_final: 0.7493 (mtt) REVERT: F 75 MET cc_start: 0.4786 (ptt) cc_final: 0.4536 (ptt) REVERT: F 105 MET cc_start: 0.5292 (ptt) cc_final: 0.4861 (mmt) REVERT: G 6 MET cc_start: 0.5985 (OUTLIER) cc_final: 0.5117 (ppp) REVERT: H 98 ASN cc_start: 0.8224 (m110) cc_final: 0.7584 (t0) outliers start: 60 outliers final: 46 residues processed: 293 average time/residue: 0.1110 time to fit residues: 48.2402 Evaluate side-chains 274 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 62 LYS Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain H residue 90 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 84 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 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 = 0.4508 r_free = 0.4508 target = 0.195231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.160904 restraints weight = 25102.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152778 restraints weight = 40546.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.150582 restraints weight = 35770.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151216 restraints weight = 31323.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.150333 restraints weight = 22851.832| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14839 Z= 0.175 Angle : 0.712 13.468 19996 Z= 0.367 Chirality : 0.042 0.156 2202 Planarity : 0.005 0.139 2539 Dihedral : 4.692 25.066 1913 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.40 % Allowed : 20.30 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1738 helix: 0.84 (0.16), residues: 1040 sheet: 0.93 (0.50), residues: 104 loop : -0.53 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 86 TYR 0.036 0.002 TYR F 79 PHE 0.055 0.002 PHE D 39 TRP 0.031 0.002 TRP D 14 HIS 0.010 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00403 (14819) covalent geometry : angle 0.71033 (19990) hydrogen bonds : bond 0.04757 ( 816) hydrogen bonds : angle 5.08400 ( 2406) metal coordination : bond 0.00903 ( 20) metal coordination : angle 3.19113 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8204 (t80) cc_final: 0.7987 (t80) REVERT: A 234 GLN cc_start: 0.6795 (mt0) cc_final: 0.6302 (mm-40) REVERT: A 300 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7655 (tp) REVERT: A 448 SER cc_start: 0.8567 (p) cc_final: 0.8273 (m) REVERT: A 476 MET cc_start: 0.8794 (mmm) cc_final: 0.7068 (mtt) REVERT: A 544 TYR cc_start: 0.8020 (t80) cc_final: 0.7784 (t80) REVERT: A 566 MET cc_start: 0.4128 (mtm) cc_final: 0.0647 (mmp) REVERT: C 33 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7447 (mmp80) REVERT: B 22 SER cc_start: 0.6967 (m) cc_final: 0.6555 (m) REVERT: D 146 MET cc_start: 0.7434 (ppp) cc_final: 0.7174 (ppp) REVERT: D 166 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6753 (tp30) REVERT: D 170 ASP cc_start: 0.7409 (t0) cc_final: 0.7147 (t0) REVERT: D 234 GLN cc_start: 0.6695 (mt0) cc_final: 0.6203 (mm-40) REVERT: D 293 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.6884 (t70) REVERT: D 300 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7612 (tp) REVERT: D 476 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7511 (mtt) REVERT: F 75 MET cc_start: 0.4722 (ptt) cc_final: 0.4476 (ptt) REVERT: F 105 MET cc_start: 0.5093 (ptt) cc_final: 0.4747 (mmt) REVERT: G 6 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.4059 (ppp) REVERT: H 25 LYS cc_start: 0.6527 (tptt) cc_final: 0.5662 (tppt) outliers start: 55 outliers final: 40 residues processed: 283 average time/residue: 0.1156 time to fit residues: 48.4781 Evaluate side-chains 275 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 94 CYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 476 MET Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 32 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 129 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 111 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 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 = 0.4510 r_free = 0.4510 target = 0.195139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160567 restraints weight = 25229.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.153806 restraints weight = 41723.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.152929 restraints weight = 34571.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.153448 restraints weight = 32509.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.153026 restraints weight = 24580.458| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14839 Z= 0.164 Angle : 0.713 12.805 19996 Z= 0.364 Chirality : 0.042 0.188 2202 Planarity : 0.005 0.142 2539 Dihedral : 4.692 28.392 1913 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.03 % Allowed : 21.16 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.20), residues: 1738 helix: 0.89 (0.16), residues: 1038 sheet: 0.94 (0.51), residues: 104 loop : -0.58 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 86 TYR 0.035 0.002 TYR D 43 PHE 0.060 0.002 PHE D 39 TRP 0.028 0.002 TRP D 14 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00373 (14819) covalent geometry : angle 0.71183 (19990) hydrogen bonds : bond 0.04552 ( 816) hydrogen bonds : angle 5.03107 ( 2406) metal coordination : bond 0.00924 ( 20) metal coordination : angle 2.26795 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 244 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8308 (t80) cc_final: 0.8102 (t80) REVERT: A 234 GLN cc_start: 0.6808 (mt0) cc_final: 0.6348 (mm-40) REVERT: A 300 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7668 (tp) REVERT: A 448 SER cc_start: 0.8635 (p) cc_final: 0.8206 (m) REVERT: A 451 MET cc_start: 0.7709 (mmp) cc_final: 0.7413 (mmp) REVERT: A 476 MET cc_start: 0.8766 (mmm) cc_final: 0.7101 (mtt) REVERT: A 544 TYR cc_start: 0.7985 (t80) cc_final: 0.7758 (t80) REVERT: A 566 MET cc_start: 0.3898 (mtm) cc_final: 0.0777 (mmp) REVERT: A 621 LYS cc_start: 0.7354 (tptt) cc_final: 0.7064 (tptp) REVERT: B 22 SER cc_start: 0.6953 (m) cc_final: 0.6533 (m) REVERT: D 62 LYS cc_start: 0.8145 (mttp) cc_final: 0.7632 (tppt) REVERT: D 234 GLN cc_start: 0.6688 (mt0) cc_final: 0.6127 (mm-40) REVERT: D 293 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.6801 (t70) REVERT: D 300 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7619 (tp) REVERT: D 476 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7807 (mtt) REVERT: F 75 MET cc_start: 0.4827 (ptt) cc_final: 0.4158 (ppp) REVERT: F 105 MET cc_start: 0.4983 (ptt) cc_final: 0.4652 (mmt) REVERT: G 6 MET cc_start: 0.5070 (OUTLIER) cc_final: 0.4358 (ppp) REVERT: H 25 LYS cc_start: 0.6553 (tptt) cc_final: 0.5688 (tppt) REVERT: H 98 ASN cc_start: 0.8260 (m-40) cc_final: 0.7688 (t0) outliers start: 49 outliers final: 37 residues processed: 284 average time/residue: 0.1129 time to fit residues: 47.6575 Evaluate side-chains 265 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 547 HIS Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 476 MET Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 32 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 78 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 166 optimal weight: 5.9990 chunk 146 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 0.0170 chunk 28 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 320 HIS D 169 ASN ** D 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.196750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159150 restraints weight = 25168.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152911 restraints weight = 42350.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.152808 restraints weight = 33292.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.151559 restraints weight = 28492.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151953 restraints weight = 24885.712| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.7160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14839 Z= 0.148 Angle : 0.737 18.148 19996 Z= 0.370 Chirality : 0.041 0.154 2202 Planarity : 0.005 0.064 2539 Dihedral : 4.662 27.957 1913 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.54 % Allowed : 22.52 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1738 helix: 0.90 (0.16), residues: 1038 sheet: 0.93 (0.50), residues: 104 loop : -0.55 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 86 TYR 0.043 0.002 TYR A 107 PHE 0.064 0.002 PHE D 39 TRP 0.027 0.002 TRP D 14 HIS 0.005 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00330 (14819) covalent geometry : angle 0.73608 (19990) hydrogen bonds : bond 0.04440 ( 816) hydrogen bonds : angle 4.95729 ( 2406) metal coordination : bond 0.00721 ( 20) metal coordination : angle 2.46084 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3476 Ramachandran restraints generated. 1738 Oldfield, 0 Emsley, 1738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 248 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8299 (t80) cc_final: 0.8091 (t80) REVERT: A 177 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7832 (p0) REVERT: A 300 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7615 (tp) REVERT: A 320 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8292 (t-90) REVERT: A 448 SER cc_start: 0.8674 (p) cc_final: 0.8221 (m) REVERT: A 476 MET cc_start: 0.8761 (mmm) cc_final: 0.7144 (mtt) REVERT: A 544 TYR cc_start: 0.7923 (t80) cc_final: 0.7663 (t80) REVERT: A 566 MET cc_start: 0.3591 (mtm) cc_final: 0.0672 (mmp) REVERT: B 22 SER cc_start: 0.6881 (m) cc_final: 0.6418 (m) REVERT: D 62 LYS cc_start: 0.8155 (mttp) cc_final: 0.7651 (tppt) REVERT: D 234 GLN cc_start: 0.6615 (mt0) cc_final: 0.6118 (mm-40) REVERT: D 293 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6694 (t70) REVERT: D 300 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (tp) REVERT: D 476 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7410 (mtt) REVERT: D 561 THR cc_start: 0.8716 (p) cc_final: 0.8468 (p) REVERT: D 621 LYS cc_start: 0.7785 (tptt) cc_final: 0.7517 (tptt) REVERT: F 75 MET cc_start: 0.4839 (ptt) cc_final: 0.4152 (ppp) REVERT: F 105 MET cc_start: 0.5041 (ptt) cc_final: 0.4667 (mmt) REVERT: G 6 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.4793 (ppp) REVERT: H 25 LYS cc_start: 0.6590 (tptt) cc_final: 0.5705 (tppt) REVERT: H 52 LEU cc_start: 0.5600 (tp) cc_final: 0.5390 (tp) REVERT: H 98 ASN cc_start: 0.8119 (m-40) cc_final: 0.7672 (t0) outliers start: 41 outliers final: 29 residues processed: 278 average time/residue: 0.1231 time to fit residues: 50.0747 Evaluate side-chains 270 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 SER Chi-restraints excluded: chain A residue 71 HIS Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain E residue 33 TRP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 71 HIS Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 476 MET Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 547 HIS Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain H residue 82 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 51 optimal weight: 0.1980 chunk 168 optimal weight: 9.9990 chunk 166 optimal weight: 0.0070 chunk 64 optimal weight: 5.9990 chunk 140 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN A 320 HIS ** H 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 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 = 0.4542 r_free = 0.4542 target = 0.197876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159357 restraints weight = 24959.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153120 restraints weight = 40641.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.153193 restraints weight = 31437.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.151776 restraints weight = 29143.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152542 restraints weight = 23021.496| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14839 Z= 0.143 Angle : 0.724 13.726 19996 Z= 0.363 Chirality : 0.041 0.204 2202 Planarity : 0.005 0.068 2539 Dihedral : 4.662 27.592 1913 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.23 % Allowed : 23.14 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1738 helix: 0.94 (0.16), residues: 1038 sheet: 0.92 (0.51), residues: 104 loop : -0.58 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 86 TYR 0.040 0.002 TYR D 43 PHE 0.066 0.002 PHE D 39 TRP 0.024 0.002 TRP D 14 HIS 0.026 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00314 (14819) covalent geometry : angle 0.72259 (19990) hydrogen bonds : bond 0.04291 ( 816) hydrogen bonds : angle 4.93645 ( 2406) metal coordination : bond 0.00688 ( 20) metal coordination : angle 2.50807 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2517.58 seconds wall clock time: 44 minutes 31.17 seconds (2671.17 seconds total)