Starting phenix.real_space_refine on Sun Aug 24 06:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.map" model { file = "/net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk5_22362/08_2025/7jk5_22362.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 73 5.49 5 Mg 3 5.21 5 S 89 5.16 5 C 10879 2.51 5 N 3040 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17408 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "C" Number of atoms: 4747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4747 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 22, 'TRANS': 567} Chain breaks: 8 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3127 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 11, 'TRANS': 381} Chain breaks: 4 Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3050 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain breaks: 1 Chain: "H" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 660 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.89, per 1000 atoms: 0.28 Number of scatterers: 17408 At special positions: 0 Unit cell: (122.12, 155.66, 109.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 89 16.00 P 73 15.00 Mg 3 11.99 O 3324 8.00 N 3040 7.00 C 10879 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 745.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 11 sheets defined 65.9% alpha, 6.5% beta 32 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'B' and resid 328 through 339 removed outlier: 3.684A pdb=" N TYR B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 3.677A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 400 removed outlier: 3.906A pdb=" N MET B 393 " --> pdb=" O THR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 424 removed outlier: 4.009A pdb=" N LEU B 424 " --> pdb=" O GLU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.661A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 removed outlier: 3.748A pdb=" N LEU B 473 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.705A pdb=" N PHE B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.603A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 88 removed outlier: 4.109A pdb=" N GLU C 51 " --> pdb=" O GLN C 47 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.915A pdb=" N LEU C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 139 through 159 Processing helix chain 'C' and resid 184 through 196 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.883A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 310 through 327 Processing helix chain 'C' and resid 328 through 335 removed outlier: 5.779A pdb=" N ALA C 331 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE C 332 " --> pdb=" O GLY C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 358 Processing helix chain 'C' and resid 361 through 368 removed outlier: 4.310A pdb=" N TYR C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 381 removed outlier: 3.520A pdb=" N THR C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 416 Proline residue: C 390 - end of helix removed outlier: 4.079A pdb=" N ASP C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.501A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 440 removed outlier: 3.539A pdb=" N SER C 440 " --> pdb=" O ALA C 437 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 437 through 440' Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.563A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 477 Processing helix chain 'C' and resid 484 through 507 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 removed outlier: 3.754A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 620 Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 655 removed outlier: 3.762A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 672 Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 Processing helix chain 'D' and resid 29 through 46 removed outlier: 3.552A pdb=" N SER D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 74 Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.512A pdb=" N ASN D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 78 through 82' Processing helix chain 'D' and resid 95 through 107 removed outlier: 3.723A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 135 removed outlier: 3.505A pdb=" N ALA D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 154 removed outlier: 3.669A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.690A pdb=" N TYR D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.593A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 281 removed outlier: 3.612A pdb=" N THR D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.719A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.540A pdb=" N MET D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 341 removed outlier: 3.511A pdb=" N CYS D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.971A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.834A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.754A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 455 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 76 through 89 removed outlier: 3.804A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.681A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 96' Processing helix chain 'E' and resid 100 through 110 Processing helix chain 'E' and resid 114 through 118 removed outlier: 3.756A pdb=" N GLU E 117 " --> pdb=" O THR E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 131 Processing helix chain 'E' and resid 137 through 144 removed outlier: 3.525A pdb=" N ARG E 144 " --> pdb=" O PRO E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 167 removed outlier: 4.085A pdb=" N TYR E 167 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 removed outlier: 4.117A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.915A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 236 through 240 removed outlier: 4.078A pdb=" N LYS E 239 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.257A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 264 Processing helix chain 'E' and resid 275 through 287 Proline residue: E 282 - end of helix removed outlier: 3.812A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 342 through 347 Processing helix chain 'E' and resid 382 through 394 removed outlier: 4.032A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 3.778A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 428 removed outlier: 3.986A pdb=" N ILE E 425 " --> pdb=" O GLU E 422 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET E 426 " --> pdb=" O GLN E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.756A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 236 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.672A pdb=" N SER A 548 " --> pdb=" O LYS A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 588 removed outlier: 3.943A pdb=" N ASP A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.544A pdb=" N GLN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 637 No H-bonds generated for 'chain 'A' and resid 635 through 637' Processing helix chain 'A' and resid 639 through 641 No H-bonds generated for 'chain 'A' and resid 639 through 641' Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.784A pdb=" N TYR A 648 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 670 Processing helix chain 'A' and resid 686 through 690 Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 746 through 758 removed outlier: 3.860A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 4.055A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 3.529A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 removed outlier: 3.549A pdb=" N VAL A 810 " --> pdb=" O THR A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.521A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'A' and resid 874 through 888 Processing helix chain 'A' and resid 895 through 899 removed outlier: 3.787A pdb=" N ASN A 898 " --> pdb=" O HIS A 895 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 899 " --> pdb=" O SER A 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 899' Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.805A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 377 through 382 removed outlier: 5.946A pdb=" N THR B 377 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 433 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU B 379 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N HIS B 435 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 381 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B 430 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N LEU B 463 " --> pdb=" O LEU B 430 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 432 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 101 removed outlier: 6.512A pdb=" N LEU C 96 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG C 264 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C 98 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 266 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 100 " --> pdb=" O PHE C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.343A pdb=" N MET C 128 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE C 208 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N CYS C 130 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 205 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL C 239 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 207 " --> pdb=" O VAL C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 658 through 659 Processing sheet with id=AA5, first strand: chain 'D' and resid 83 through 88 removed outlier: 6.711A pdb=" N LEU D 84 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE D 145 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 86 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLU D 147 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 88 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN D 50 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLY D 179 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU D 52 " --> pdb=" O GLY D 179 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N THR D 181 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 54 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 112 through 113 Processing sheet with id=AA7, first strand: chain 'D' and resid 406 through 408 Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 70 removed outlier: 6.615A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 380 through 381 removed outlier: 6.902A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 628 through 633 removed outlier: 3.614A pdb=" N VAL A 680 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 684 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 712 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 852 through 853 removed outlier: 3.514A pdb=" N ILE A 892 " --> pdb=" O LEU A 905 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4838 1.34 - 1.46: 3698 1.46 - 1.58: 9050 1.58 - 1.70: 141 1.70 - 1.82: 129 Bond restraints: 17856 Sorted by residual: bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.56e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" C5 ATP A1001 " pdb=" C6 ATP A1001 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.00e-02 1.00e+04 3.06e+01 ... (remaining 17851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 24252 4.68 - 9.36: 161 9.36 - 14.03: 6 14.03 - 18.71: 1 18.71 - 23.39: 5 Bond angle restraints: 24425 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 116.48 23.39 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 118.21 21.66 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 118.61 21.26 1.00e+00 1.00e+00 4.52e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 115.70 21.13 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 117.14 19.69 1.00e+00 1.00e+00 3.88e+02 ... (remaining 24420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8961 17.81 - 35.62: 1190 35.62 - 53.43: 440 53.43 - 71.24: 129 71.24 - 89.05: 25 Dihedral angle restraints: 10745 sinusoidal: 4871 harmonic: 5874 Sorted by residual: dihedral pdb=" CA ALA E 136 " pdb=" C ALA E 136 " pdb=" N ASN E 137 " pdb=" CA ASN E 137 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASP C 337 " pdb=" C ASP C 337 " pdb=" N TYR C 338 " pdb=" CA TYR C 338 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N THR D 159 " pdb=" CA THR D 159 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 10742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1866 0.052 - 0.104: 751 0.104 - 0.155: 150 0.155 - 0.207: 35 0.207 - 0.259: 9 Chirality restraints: 2811 Sorted by residual: chirality pdb=" CA GLU E 9 " pdb=" N GLU E 9 " pdb=" C GLU E 9 " pdb=" CB GLU E 9 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ARG C 419 " pdb=" N ARG C 419 " pdb=" C ARG C 419 " pdb=" CB ARG C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2808 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 485 " -0.030 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE B 485 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 485 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 485 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 485 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 485 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 485 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 237 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C VAL C 237 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 237 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 238 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 639 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 640 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 640 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 640 " 0.039 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 176 2.62 - 3.19: 14363 3.19 - 3.76: 28609 3.76 - 4.33: 37010 4.33 - 4.90: 58829 Nonbonded interactions: 138987 Sorted by model distance: nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.049 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 902 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 2.103 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.104 2.170 nonbonded pdb=" O3G ATP A1001 " pdb="MG MG A1002 " model vdw 2.122 2.170 ... (remaining 138982 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.000 Find NCS groups from input model: 0.110 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.007 0.076 17857 Z= 0.355 Angle : 1.118 23.391 24425 Z= 0.701 Chirality : 0.058 0.259 2811 Planarity : 0.007 0.071 2871 Dihedral : 19.285 89.048 6911 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.29 % Allowed : 6.00 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.16), residues: 1961 helix: -2.63 (0.10), residues: 1180 sheet: -3.42 (0.32), residues: 156 loop : 0.32 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 213 TYR 0.030 0.003 TYR C 255 PHE 0.055 0.003 PHE B 485 TRP 0.030 0.003 TRP C 191 HIS 0.009 0.002 HIS C 622 Details of bonding type rmsd covalent geometry : bond 0.00692 (17856) covalent geometry : angle 1.11841 (24425) hydrogen bonds : bond 0.14145 ( 911) hydrogen bonds : angle 6.79023 ( 2577) Misc. bond : bond 0.00271 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 300 time to evaluate : 0.650 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: B 335 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9029 (mp0) REVERT: B 342 LYS cc_start: 0.9573 (tttm) cc_final: 0.9087 (ptpp) REVERT: B 343 TRP cc_start: 0.9286 (m-10) cc_final: 0.8883 (m100) REVERT: B 417 MET cc_start: 0.9126 (mmt) cc_final: 0.8745 (ptt) REVERT: B 421 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8289 (mt-10) REVERT: B 474 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8596 (pp) REVERT: B 483 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8530 (m-80) REVERT: B 493 MET cc_start: 0.7992 (mmt) cc_final: 0.7064 (tmm) REVERT: C 208 ILE cc_start: 0.9557 (mt) cc_final: 0.9324 (tp) REVERT: C 246 MET cc_start: 0.8117 (mmm) cc_final: 0.7876 (tpp) REVERT: C 323 MET cc_start: 0.9339 (tmm) cc_final: 0.9061 (tmm) REVERT: C 340 LYS cc_start: 0.9733 (tptp) cc_final: 0.9453 (tptm) REVERT: C 381 ASP cc_start: 0.9154 (t0) cc_final: 0.8940 (t0) REVERT: C 395 ASP cc_start: 0.9198 (t70) cc_final: 0.8816 (p0) REVERT: C 623 PHE cc_start: 0.9144 (t80) cc_final: 0.8696 (t80) REVERT: D 215 TYR cc_start: 0.8724 (t80) cc_final: 0.8486 (t80) REVERT: D 335 ASP cc_start: 0.9079 (m-30) cc_final: 0.8678 (p0) REVERT: D 341 CYS cc_start: 0.8910 (m) cc_final: 0.8660 (m) REVERT: D 346 LEU cc_start: 0.9418 (tp) cc_final: 0.9151 (tt) REVERT: D 409 LEU cc_start: 0.8844 (mt) cc_final: 0.8584 (mp) REVERT: D 421 GLN cc_start: 0.8783 (mt0) cc_final: 0.8094 (mp10) REVERT: D 426 MET cc_start: 0.9325 (mmm) cc_final: 0.9050 (mmm) REVERT: D 440 MET cc_start: 0.8961 (mmt) cc_final: 0.8679 (mmm) REVERT: E 69 LEU cc_start: 0.8989 (tp) cc_final: 0.7655 (tp) REVERT: E 80 MET cc_start: 0.9401 (ttm) cc_final: 0.9116 (tpp) REVERT: E 84 LEU cc_start: 0.9721 (mt) cc_final: 0.9518 (mt) REVERT: E 237 PHE cc_start: 0.8490 (m-10) cc_final: 0.8056 (m-10) REVERT: A 588 ASP cc_start: 0.8686 (m-30) cc_final: 0.8189 (p0) REVERT: A 790 CYS cc_start: 0.9594 (m) cc_final: 0.9366 (m) REVERT: A 795 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8684 (mt-10) outliers start: 5 outliers final: 1 residues processed: 304 average time/residue: 0.1586 time to fit residues: 70.9350 Evaluate side-chains 182 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN B 363 GLN B 461 HIS ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 204 GLN C 221 GLN C 250 HIS C 591 HIS C 715 HIS D 35 ASN D 242 GLN D 274 GLN D 399 HIS D 437 HIS E 202 GLN ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 433 GLN A 662 HIS A 809 HIS A 838 GLN A 902 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.062789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.045245 restraints weight = 88561.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046631 restraints weight = 49898.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047607 restraints weight = 33560.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048243 restraints weight = 25404.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048733 restraints weight = 20937.998| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17857 Z= 0.154 Angle : 0.709 10.065 24425 Z= 0.375 Chirality : 0.043 0.283 2811 Planarity : 0.005 0.057 2871 Dihedral : 20.055 86.354 3005 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.88 % Allowed : 13.31 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.18), residues: 1961 helix: -0.51 (0.13), residues: 1193 sheet: -2.72 (0.33), residues: 169 loop : 0.14 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 277 TYR 0.021 0.002 TYR C 255 PHE 0.018 0.002 PHE C 362 TRP 0.023 0.002 TRP C 191 HIS 0.008 0.001 HIS A 914 Details of bonding type rmsd covalent geometry : bond 0.00335 (17856) covalent geometry : angle 0.70855 (24425) hydrogen bonds : bond 0.04397 ( 911) hydrogen bonds : angle 4.92997 ( 2577) Misc. bond : bond 0.00158 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.704 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: B 335 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8912 (mp0) REVERT: B 342 LYS cc_start: 0.9476 (tttm) cc_final: 0.9075 (ptpp) REVERT: B 343 TRP cc_start: 0.9217 (m-10) cc_final: 0.8704 (m100) REVERT: B 421 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 483 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8353 (m-10) REVERT: B 493 MET cc_start: 0.8031 (mmt) cc_final: 0.7037 (tmm) REVERT: C 132 LEU cc_start: 0.9307 (tp) cc_final: 0.9065 (tp) REVERT: C 208 ILE cc_start: 0.9612 (mt) cc_final: 0.9367 (tp) REVERT: C 323 MET cc_start: 0.9253 (tmm) cc_final: 0.8980 (tmm) REVERT: C 340 LYS cc_start: 0.9736 (tptp) cc_final: 0.9446 (tptp) REVERT: C 395 ASP cc_start: 0.9156 (t70) cc_final: 0.8794 (p0) REVERT: C 658 MET cc_start: 0.9015 (tpt) cc_final: 0.8751 (tpt) REVERT: D 46 MET cc_start: 0.9252 (mpp) cc_final: 0.8885 (mpp) REVERT: D 335 ASP cc_start: 0.8825 (m-30) cc_final: 0.8386 (p0) REVERT: D 409 LEU cc_start: 0.8912 (mt) cc_final: 0.8567 (mp) REVERT: D 426 MET cc_start: 0.9239 (mmm) cc_final: 0.8879 (mmm) REVERT: E 69 LEU cc_start: 0.9127 (tp) cc_final: 0.8921 (tp) REVERT: E 164 GLU cc_start: 0.8848 (mp0) cc_final: 0.8415 (mp0) REVERT: E 237 PHE cc_start: 0.8544 (m-10) cc_final: 0.8000 (m-10) REVERT: A 588 ASP cc_start: 0.8577 (m-30) cc_final: 0.8134 (p0) REVERT: A 790 CYS cc_start: 0.9591 (m) cc_final: 0.9377 (m) REVERT: A 795 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8696 (mt-10) REVERT: A 828 ASN cc_start: 0.9300 (t0) cc_final: 0.8964 (t0) REVERT: A 855 MET cc_start: 0.8915 (ptm) cc_final: 0.8666 (ptp) outliers start: 33 outliers final: 16 residues processed: 225 average time/residue: 0.1472 time to fit residues: 50.4553 Evaluate side-chains 185 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 146 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 196 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS C 570 GLN C 585 GLN D 20 GLN D 200 HIS A 577 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.043605 restraints weight = 89247.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.044968 restraints weight = 50823.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045915 restraints weight = 34350.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046556 restraints weight = 26044.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.046967 restraints weight = 21413.940| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17857 Z= 0.171 Angle : 0.672 9.512 24425 Z= 0.354 Chirality : 0.042 0.259 2811 Planarity : 0.004 0.061 2871 Dihedral : 19.923 84.204 3003 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.28 % Allowed : 14.96 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.19), residues: 1961 helix: 0.32 (0.15), residues: 1199 sheet: -2.80 (0.33), residues: 177 loop : 0.22 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 613 TYR 0.018 0.001 TYR A 579 PHE 0.020 0.001 PHE C 362 TRP 0.019 0.002 TRP C 191 HIS 0.007 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00372 (17856) covalent geometry : angle 0.67183 (24425) hydrogen bonds : bond 0.04141 ( 911) hydrogen bonds : angle 4.67578 ( 2577) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8963 (mp0) REVERT: B 342 LYS cc_start: 0.9467 (tttm) cc_final: 0.9079 (ptpp) REVERT: B 343 TRP cc_start: 0.9221 (m-10) cc_final: 0.8728 (m100) REVERT: B 438 ASP cc_start: 0.8118 (p0) cc_final: 0.7823 (p0) REVERT: B 443 ARG cc_start: 0.9014 (mtt90) cc_final: 0.8782 (mmt90) REVERT: B 479 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8956 (ptpp) REVERT: B 483 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8378 (m-10) REVERT: B 493 MET cc_start: 0.8096 (mmt) cc_final: 0.7122 (tmm) REVERT: C 132 LEU cc_start: 0.9286 (tp) cc_final: 0.8949 (tp) REVERT: C 208 ILE cc_start: 0.9624 (mt) cc_final: 0.9355 (tp) REVERT: C 222 ASP cc_start: 0.9186 (m-30) cc_final: 0.8865 (p0) REVERT: C 323 MET cc_start: 0.9227 (tmm) cc_final: 0.8950 (tmm) REVERT: C 340 LYS cc_start: 0.9734 (tptp) cc_final: 0.9316 (tptp) REVERT: C 658 MET cc_start: 0.8920 (tpt) cc_final: 0.8674 (tpt) REVERT: D 335 ASP cc_start: 0.8868 (m-30) cc_final: 0.8516 (p0) REVERT: D 407 MET cc_start: 0.8487 (ptp) cc_final: 0.8225 (mpp) REVERT: D 409 LEU cc_start: 0.8929 (mt) cc_final: 0.8627 (mp) REVERT: D 426 MET cc_start: 0.9271 (mmm) cc_final: 0.8816 (mmm) REVERT: E 237 PHE cc_start: 0.8575 (m-10) cc_final: 0.8039 (m-10) REVERT: A 524 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8517 (ptp) REVERT: A 528 ARG cc_start: 0.8765 (tpt-90) cc_final: 0.8537 (tpt90) REVERT: A 588 ASP cc_start: 0.8588 (m-30) cc_final: 0.8168 (p0) REVERT: A 630 LEU cc_start: 0.9032 (tp) cc_final: 0.8776 (tp) REVERT: A 790 CYS cc_start: 0.9626 (m) cc_final: 0.9407 (m) REVERT: A 795 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8591 (mp0) REVERT: A 828 ASN cc_start: 0.9262 (t0) cc_final: 0.9018 (t0) REVERT: A 855 MET cc_start: 0.8950 (ptm) cc_final: 0.8707 (ptp) outliers start: 40 outliers final: 19 residues processed: 199 average time/residue: 0.1351 time to fit residues: 42.3014 Evaluate side-chains 182 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN B 477 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.042989 restraints weight = 89461.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.044314 restraints weight = 50756.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.045205 restraints weight = 34439.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045847 restraints weight = 26337.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046273 restraints weight = 21683.595| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17857 Z= 0.177 Angle : 0.657 12.234 24425 Z= 0.345 Chirality : 0.041 0.268 2811 Planarity : 0.004 0.054 2871 Dihedral : 19.845 87.315 3003 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 15.59 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.19), residues: 1961 helix: 0.73 (0.15), residues: 1194 sheet: -2.71 (0.34), residues: 177 loop : 0.24 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.021 0.001 TYR A 698 PHE 0.019 0.001 PHE C 362 TRP 0.020 0.002 TRP C 57 HIS 0.007 0.001 HIS C 615 Details of bonding type rmsd covalent geometry : bond 0.00378 (17856) covalent geometry : angle 0.65747 (24425) hydrogen bonds : bond 0.04043 ( 911) hydrogen bonds : angle 4.53905 ( 2577) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 0.682 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: B 335 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9021 (mm-30) REVERT: B 342 LYS cc_start: 0.9414 (tttm) cc_final: 0.9028 (mtmm) REVERT: B 343 TRP cc_start: 0.9258 (m-10) cc_final: 0.8729 (m100) REVERT: B 479 LYS cc_start: 0.9257 (ptpp) cc_final: 0.9036 (ptpp) REVERT: B 483 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8402 (m-10) REVERT: B 493 MET cc_start: 0.8148 (mmt) cc_final: 0.7296 (tmm) REVERT: C 132 LEU cc_start: 0.9311 (tp) cc_final: 0.8945 (tp) REVERT: C 208 ILE cc_start: 0.9597 (mt) cc_final: 0.9366 (tp) REVERT: C 323 MET cc_start: 0.9194 (tmm) cc_final: 0.8917 (tmm) REVERT: C 395 ASP cc_start: 0.8879 (m-30) cc_final: 0.8213 (p0) REVERT: D 335 ASP cc_start: 0.8869 (m-30) cc_final: 0.8517 (p0) REVERT: D 407 MET cc_start: 0.8468 (ptp) cc_final: 0.8148 (mpp) REVERT: D 426 MET cc_start: 0.9275 (mmm) cc_final: 0.8898 (mmm) REVERT: E 143 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9434 (mm) REVERT: E 237 PHE cc_start: 0.8608 (m-10) cc_final: 0.8060 (m-10) REVERT: A 524 MET cc_start: 0.9116 (tpt) cc_final: 0.8480 (ptp) REVERT: A 528 ARG cc_start: 0.8813 (tpt-90) cc_final: 0.8554 (tpt90) REVERT: A 588 ASP cc_start: 0.8602 (m-30) cc_final: 0.8170 (p0) REVERT: A 630 LEU cc_start: 0.9057 (tp) cc_final: 0.8765 (tp) REVERT: A 750 LEU cc_start: 0.9528 (mt) cc_final: 0.8694 (tp) REVERT: A 790 CYS cc_start: 0.9639 (m) cc_final: 0.9418 (m) REVERT: A 828 ASN cc_start: 0.9221 (t0) cc_final: 0.8979 (t0) outliers start: 39 outliers final: 25 residues processed: 191 average time/residue: 0.1370 time to fit residues: 40.9181 Evaluate side-chains 180 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.059335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.042303 restraints weight = 89449.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043617 restraints weight = 50787.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044521 restraints weight = 34503.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.045127 restraints weight = 26285.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.045531 restraints weight = 21721.785| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17857 Z= 0.209 Angle : 0.657 9.455 24425 Z= 0.346 Chirality : 0.041 0.165 2811 Planarity : 0.004 0.053 2871 Dihedral : 19.823 89.858 3003 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.46 % Allowed : 16.90 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.19), residues: 1961 helix: 0.93 (0.15), residues: 1190 sheet: -2.58 (0.35), residues: 171 loop : 0.12 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.020 0.002 TYR A 579 PHE 0.018 0.002 PHE C 362 TRP 0.019 0.002 TRP C 57 HIS 0.015 0.001 HIS D 200 Details of bonding type rmsd covalent geometry : bond 0.00446 (17856) covalent geometry : angle 0.65743 (24425) hydrogen bonds : bond 0.04224 ( 911) hydrogen bonds : angle 4.50777 ( 2577) Misc. bond : bond 0.00075 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.9416 (tttm) cc_final: 0.9064 (mtmm) REVERT: B 343 TRP cc_start: 0.9242 (m-10) cc_final: 0.8747 (m100) REVERT: B 441 MET cc_start: 0.8897 (mtp) cc_final: 0.8570 (pmm) REVERT: B 493 MET cc_start: 0.8394 (mmt) cc_final: 0.7209 (tmm) REVERT: C 132 LEU cc_start: 0.9307 (tp) cc_final: 0.8917 (tp) REVERT: C 208 ILE cc_start: 0.9584 (mt) cc_final: 0.9327 (tp) REVERT: C 222 ASP cc_start: 0.9209 (m-30) cc_final: 0.8870 (p0) REVERT: C 323 MET cc_start: 0.9191 (tmm) cc_final: 0.8920 (tmm) REVERT: C 395 ASP cc_start: 0.8848 (m-30) cc_final: 0.8187 (p0) REVERT: D 53 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9284 (mt) REVERT: D 335 ASP cc_start: 0.8928 (m-30) cc_final: 0.8549 (p0) REVERT: D 347 GLU cc_start: 0.8830 (mp0) cc_final: 0.8546 (mp0) REVERT: D 426 MET cc_start: 0.9273 (mmm) cc_final: 0.8792 (mmm) REVERT: E 175 ILE cc_start: 0.9559 (tt) cc_final: 0.9145 (mt) REVERT: E 237 PHE cc_start: 0.8642 (m-10) cc_final: 0.8129 (m-10) REVERT: A 524 MET cc_start: 0.9129 (tpt) cc_final: 0.8476 (ptp) REVERT: A 528 ARG cc_start: 0.8757 (tpt-90) cc_final: 0.8484 (tpt90) REVERT: A 588 ASP cc_start: 0.8664 (m-30) cc_final: 0.8216 (p0) REVERT: A 630 LEU cc_start: 0.9087 (tp) cc_final: 0.8779 (tp) REVERT: A 750 LEU cc_start: 0.9527 (mt) cc_final: 0.8644 (tt) REVERT: A 790 CYS cc_start: 0.9640 (m) cc_final: 0.9430 (m) REVERT: A 828 ASN cc_start: 0.9234 (t0) cc_final: 0.8986 (t0) outliers start: 43 outliers final: 31 residues processed: 191 average time/residue: 0.1339 time to fit residues: 40.1044 Evaluate side-chains 179 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 444 ILE Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 99 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 199 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.059605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042629 restraints weight = 89096.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.043924 restraints weight = 50914.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044831 restraints weight = 34710.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045434 restraints weight = 26417.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045820 restraints weight = 21777.409| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17857 Z= 0.165 Angle : 0.661 11.777 24425 Z= 0.341 Chirality : 0.042 0.340 2811 Planarity : 0.004 0.056 2871 Dihedral : 19.743 90.972 3003 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.28 % Allowed : 17.82 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.20), residues: 1961 helix: 1.06 (0.15), residues: 1193 sheet: -2.51 (0.36), residues: 169 loop : 0.13 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 636 TYR 0.022 0.001 TYR A 579 PHE 0.018 0.001 PHE C 362 TRP 0.015 0.001 TRP C 57 HIS 0.006 0.001 HIS C 615 Details of bonding type rmsd covalent geometry : bond 0.00356 (17856) covalent geometry : angle 0.66088 (24425) hydrogen bonds : bond 0.03802 ( 911) hydrogen bonds : angle 4.43657 ( 2577) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.695 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: B 342 LYS cc_start: 0.9400 (tttm) cc_final: 0.9061 (mtmm) REVERT: B 343 TRP cc_start: 0.9177 (m-10) cc_final: 0.8648 (m100) REVERT: B 344 MET cc_start: 0.9009 (ptt) cc_final: 0.8734 (ptp) REVERT: B 441 MET cc_start: 0.8908 (mtp) cc_final: 0.8592 (pmm) REVERT: B 493 MET cc_start: 0.8414 (mmt) cc_final: 0.7049 (tmm) REVERT: C 132 LEU cc_start: 0.9272 (tp) cc_final: 0.8875 (tp) REVERT: C 185 MET cc_start: 0.8542 (tpp) cc_final: 0.8332 (tpp) REVERT: C 208 ILE cc_start: 0.9585 (mt) cc_final: 0.9320 (tp) REVERT: C 222 ASP cc_start: 0.9185 (m-30) cc_final: 0.8845 (p0) REVERT: C 323 MET cc_start: 0.9172 (tmm) cc_final: 0.8905 (tmm) REVERT: D 335 ASP cc_start: 0.8937 (m-30) cc_final: 0.8517 (p0) REVERT: D 347 GLU cc_start: 0.8848 (mp0) cc_final: 0.8538 (mp0) REVERT: D 426 MET cc_start: 0.9279 (mmm) cc_final: 0.8726 (mmm) REVERT: E 151 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8791 (mt) REVERT: E 237 PHE cc_start: 0.8629 (m-10) cc_final: 0.8107 (m-10) REVERT: A 528 ARG cc_start: 0.8771 (tpt-90) cc_final: 0.8470 (tpt90) REVERT: A 536 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7046 (mtm) REVERT: A 588 ASP cc_start: 0.8685 (m-30) cc_final: 0.8213 (p0) REVERT: A 630 LEU cc_start: 0.9061 (tp) cc_final: 0.8848 (tp) REVERT: A 750 LEU cc_start: 0.9499 (mt) cc_final: 0.8624 (tt) REVERT: A 828 ASN cc_start: 0.9205 (t0) cc_final: 0.8939 (t0) outliers start: 40 outliers final: 31 residues processed: 187 average time/residue: 0.1365 time to fit residues: 40.2079 Evaluate side-chains 183 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 390 TYR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 67 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 181 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 191 optimal weight: 0.0070 chunk 186 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 436 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN E 412 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043866 restraints weight = 88061.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045243 restraints weight = 49757.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.046183 restraints weight = 33594.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046768 restraints weight = 25491.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.047232 restraints weight = 21150.796| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17857 Z= 0.116 Angle : 0.628 10.592 24425 Z= 0.322 Chirality : 0.041 0.316 2811 Planarity : 0.004 0.057 2871 Dihedral : 19.504 90.312 3003 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.06 % Allowed : 18.33 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.20), residues: 1961 helix: 1.22 (0.15), residues: 1186 sheet: -2.35 (0.37), residues: 169 loop : 0.14 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.024 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.016 0.001 TRP C 57 HIS 0.004 0.001 HIS A 560 Details of bonding type rmsd covalent geometry : bond 0.00248 (17856) covalent geometry : angle 0.62753 (24425) hydrogen bonds : bond 0.03368 ( 911) hydrogen bonds : angle 4.26961 ( 2577) Misc. bond : bond 0.00046 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.721 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: B 342 LYS cc_start: 0.9406 (tttm) cc_final: 0.9005 (mtmm) REVERT: B 343 TRP cc_start: 0.9110 (m-10) cc_final: 0.8609 (m100) REVERT: B 344 MET cc_start: 0.8986 (ptt) cc_final: 0.8696 (ptp) REVERT: B 441 MET cc_start: 0.8886 (mtp) cc_final: 0.8650 (pmm) REVERT: B 483 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8238 (m-10) REVERT: C 132 LEU cc_start: 0.9246 (tp) cc_final: 0.8856 (tp) REVERT: C 208 ILE cc_start: 0.9571 (mt) cc_final: 0.9337 (tp) REVERT: C 222 ASP cc_start: 0.9140 (m-30) cc_final: 0.8763 (p0) REVERT: C 223 LEU cc_start: 0.9796 (tp) cc_final: 0.9594 (tt) REVERT: C 322 LEU cc_start: 0.9624 (mm) cc_final: 0.9362 (mt) REVERT: C 323 MET cc_start: 0.9168 (tmm) cc_final: 0.8921 (tmm) REVERT: C 565 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7468 (pp) REVERT: D 335 ASP cc_start: 0.8806 (m-30) cc_final: 0.8454 (p0) REVERT: D 407 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7681 (mpp) REVERT: D 426 MET cc_start: 0.9229 (mmm) cc_final: 0.8712 (mmm) REVERT: E 69 LEU cc_start: 0.9224 (tp) cc_final: 0.8951 (tp) REVERT: E 237 PHE cc_start: 0.8470 (m-10) cc_final: 0.7990 (m-10) REVERT: A 524 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8488 (ptp) REVERT: A 528 ARG cc_start: 0.8767 (tpt-90) cc_final: 0.8446 (tpt90) REVERT: A 536 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7167 (mtm) REVERT: A 588 ASP cc_start: 0.8569 (m-30) cc_final: 0.8188 (p0) REVERT: A 750 LEU cc_start: 0.9461 (mt) cc_final: 0.8627 (tt) REVERT: A 790 CYS cc_start: 0.9633 (m) cc_final: 0.9354 (m) REVERT: A 828 ASN cc_start: 0.9152 (t0) cc_final: 0.8919 (t0) outliers start: 36 outliers final: 23 residues processed: 197 average time/residue: 0.1317 time to fit residues: 40.6476 Evaluate side-chains 182 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 59 optimal weight: 5.9990 chunk 131 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 ASN E 412 HIS A 838 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.058640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.041748 restraints weight = 91079.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.043026 restraints weight = 52266.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.043905 restraints weight = 35432.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.044468 restraints weight = 27065.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044914 restraints weight = 22523.049| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17857 Z= 0.244 Angle : 0.701 11.295 24425 Z= 0.363 Chirality : 0.042 0.258 2811 Planarity : 0.004 0.056 2871 Dihedral : 19.562 91.756 3003 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.28 % Allowed : 19.02 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1961 helix: 1.18 (0.15), residues: 1189 sheet: -2.33 (0.38), residues: 163 loop : 0.07 (0.28), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 443 TYR 0.019 0.002 TYR A 698 PHE 0.019 0.002 PHE C 362 TRP 0.026 0.002 TRP C 57 HIS 0.009 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00520 (17856) covalent geometry : angle 0.70136 (24425) hydrogen bonds : bond 0.04567 ( 911) hydrogen bonds : angle 4.45844 ( 2577) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.9437 (tttm) cc_final: 0.9084 (mtmm) REVERT: B 343 TRP cc_start: 0.9188 (m-10) cc_final: 0.8708 (m100) REVERT: B 344 MET cc_start: 0.8998 (ptt) cc_final: 0.8714 (ptp) REVERT: B 441 MET cc_start: 0.8907 (mtp) cc_final: 0.8621 (pmm) REVERT: C 132 LEU cc_start: 0.9254 (tp) cc_final: 0.8808 (tp) REVERT: C 323 MET cc_start: 0.9141 (tmm) cc_final: 0.8883 (tmm) REVERT: D 53 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9334 (mt) REVERT: D 335 ASP cc_start: 0.8912 (m-30) cc_final: 0.8545 (p0) REVERT: D 347 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8433 (mm-30) REVERT: D 407 MET cc_start: 0.8317 (mtm) cc_final: 0.7812 (mpp) REVERT: D 426 MET cc_start: 0.9249 (mmm) cc_final: 0.8717 (mmm) REVERT: E 151 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8827 (mt) REVERT: E 237 PHE cc_start: 0.8595 (m-80) cc_final: 0.8030 (m-10) REVERT: E 413 LEU cc_start: 0.9659 (mp) cc_final: 0.9438 (mt) REVERT: A 524 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8566 (tpt) REVERT: A 528 ARG cc_start: 0.8806 (tpt-90) cc_final: 0.8454 (tpt90) REVERT: A 536 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7091 (mtm) REVERT: A 588 ASP cc_start: 0.8696 (m-30) cc_final: 0.8280 (p0) REVERT: A 750 LEU cc_start: 0.9480 (mt) cc_final: 0.8677 (tt) REVERT: A 790 CYS cc_start: 0.9604 (m) cc_final: 0.9353 (m) REVERT: A 828 ASN cc_start: 0.9159 (t0) cc_final: 0.8949 (t0) outliers start: 40 outliers final: 29 residues processed: 183 average time/residue: 0.1422 time to fit residues: 40.6505 Evaluate side-chains 181 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 135 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 HIS E 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.059281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.042268 restraints weight = 90698.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.043602 restraints weight = 51181.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.044510 restraints weight = 34612.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.045073 restraints weight = 26322.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.045513 restraints weight = 21919.182| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17857 Z= 0.175 Angle : 0.683 12.886 24425 Z= 0.347 Chirality : 0.041 0.349 2811 Planarity : 0.004 0.055 2871 Dihedral : 19.637 91.081 3003 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.94 % Allowed : 19.47 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.20), residues: 1961 helix: 1.30 (0.15), residues: 1183 sheet: -2.02 (0.40), residues: 153 loop : -0.06 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 293 TYR 0.024 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.025 0.002 TRP C 57 HIS 0.006 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00381 (17856) covalent geometry : angle 0.68255 (24425) hydrogen bonds : bond 0.03797 ( 911) hydrogen bonds : angle 4.37870 ( 2577) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.649 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: B 342 LYS cc_start: 0.9433 (tttm) cc_final: 0.9085 (mtmm) REVERT: B 343 TRP cc_start: 0.9167 (m-10) cc_final: 0.8681 (m100) REVERT: B 344 MET cc_start: 0.8979 (ptt) cc_final: 0.8691 (ptp) REVERT: B 441 MET cc_start: 0.8898 (mtp) cc_final: 0.8616 (pmm) REVERT: B 493 MET cc_start: 0.8437 (mmp) cc_final: 0.8128 (mmm) REVERT: C 132 LEU cc_start: 0.9225 (tp) cc_final: 0.8760 (tp) REVERT: C 222 ASP cc_start: 0.9178 (m-30) cc_final: 0.8655 (p0) REVERT: C 323 MET cc_start: 0.9144 (tmm) cc_final: 0.8883 (tmm) REVERT: C 565 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7599 (pp) REVERT: D 53 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9302 (mt) REVERT: D 239 TYR cc_start: 0.8982 (m-10) cc_final: 0.8768 (m-10) REVERT: D 347 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 407 MET cc_start: 0.8299 (mtm) cc_final: 0.7758 (mpp) REVERT: D 426 MET cc_start: 0.9258 (mmm) cc_final: 0.8729 (mmm) REVERT: E 130 ARG cc_start: 0.9542 (mmt180) cc_final: 0.9079 (mmm-85) REVERT: E 151 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8727 (mt) REVERT: E 237 PHE cc_start: 0.8617 (m-80) cc_final: 0.8048 (m-10) REVERT: E 413 LEU cc_start: 0.9671 (mp) cc_final: 0.9460 (mt) REVERT: A 524 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8475 (tpt) REVERT: A 528 ARG cc_start: 0.8750 (tpt-90) cc_final: 0.8391 (tpt90) REVERT: A 588 ASP cc_start: 0.8720 (m-30) cc_final: 0.8304 (p0) REVERT: A 750 LEU cc_start: 0.9473 (mt) cc_final: 0.8653 (tt) REVERT: A 790 CYS cc_start: 0.9633 (m) cc_final: 0.9367 (m) REVERT: A 828 ASN cc_start: 0.9134 (t0) cc_final: 0.8894 (t0) outliers start: 34 outliers final: 27 residues processed: 180 average time/residue: 0.1185 time to fit residues: 33.3176 Evaluate side-chains 178 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 9 optimal weight: 0.0770 chunk 51 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 168 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.043412 restraints weight = 88729.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044757 restraints weight = 50134.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.045694 restraints weight = 33991.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.046252 restraints weight = 25761.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.046724 restraints weight = 21458.190| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17857 Z= 0.126 Angle : 0.660 13.405 24425 Z= 0.334 Chirality : 0.041 0.368 2811 Planarity : 0.004 0.057 2871 Dihedral : 19.474 90.128 3003 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.83 % Allowed : 19.76 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1961 helix: 1.42 (0.15), residues: 1186 sheet: -1.88 (0.41), residues: 153 loop : 0.05 (0.27), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 443 TYR 0.024 0.001 TYR A 579 PHE 0.018 0.001 PHE C 362 TRP 0.029 0.002 TRP C 57 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00276 (17856) covalent geometry : angle 0.66016 (24425) hydrogen bonds : bond 0.03399 ( 911) hydrogen bonds : angle 4.25950 ( 2577) Misc. bond : bond 0.00062 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 LYS cc_start: 0.9422 (tttm) cc_final: 0.9037 (mtmm) REVERT: B 343 TRP cc_start: 0.9130 (m-10) cc_final: 0.8646 (m100) REVERT: B 441 MET cc_start: 0.8875 (mtp) cc_final: 0.8521 (pmm) REVERT: C 132 LEU cc_start: 0.9185 (tp) cc_final: 0.8748 (tp) REVERT: C 222 ASP cc_start: 0.9133 (m-30) cc_final: 0.8785 (p0) REVERT: C 323 MET cc_start: 0.9132 (tmm) cc_final: 0.8877 (tmm) REVERT: D 239 TYR cc_start: 0.8963 (m-10) cc_final: 0.8747 (m-10) REVERT: D 385 MET cc_start: 0.9251 (mmm) cc_final: 0.8861 (mpp) REVERT: D 407 MET cc_start: 0.8243 (mtm) cc_final: 0.7707 (mpp) REVERT: D 426 MET cc_start: 0.9262 (mmm) cc_final: 0.8791 (mmm) REVERT: E 151 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8756 (mt) REVERT: E 237 PHE cc_start: 0.8527 (m-80) cc_final: 0.7972 (m-10) REVERT: A 528 ARG cc_start: 0.8756 (tpt-90) cc_final: 0.8433 (tpt90) REVERT: A 588 ASP cc_start: 0.8657 (m-30) cc_final: 0.8185 (p0) REVERT: A 750 LEU cc_start: 0.9439 (mt) cc_final: 0.8615 (tt) REVERT: A 828 ASN cc_start: 0.9063 (t0) cc_final: 0.8855 (t0) outliers start: 32 outliers final: 28 residues processed: 184 average time/residue: 0.1334 time to fit residues: 38.5486 Evaluate side-chains 179 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 703 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 160 optimal weight: 0.9980 chunk 194 optimal weight: 0.0980 chunk 145 optimal weight: 0.6980 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN E 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.043185 restraints weight = 89598.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044527 restraints weight = 50993.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.045444 restraints weight = 34603.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046013 restraints weight = 26368.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.046466 restraints weight = 21968.491| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17857 Z= 0.131 Angle : 0.670 12.372 24425 Z= 0.335 Chirality : 0.041 0.328 2811 Planarity : 0.004 0.059 2871 Dihedral : 19.392 89.759 3003 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 19.93 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.20), residues: 1961 helix: 1.45 (0.15), residues: 1192 sheet: -1.79 (0.41), residues: 153 loop : 0.07 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 37 TYR 0.026 0.001 TYR A 579 PHE 0.018 0.001 PHE C 362 TRP 0.033 0.002 TRP C 57 HIS 0.006 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00288 (17856) covalent geometry : angle 0.66975 (24425) hydrogen bonds : bond 0.03419 ( 911) hydrogen bonds : angle 4.24566 ( 2577) Misc. bond : bond 0.00053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.86 seconds wall clock time: 58 minutes 6.88 seconds (3486.88 seconds total)