Starting phenix.real_space_refine on Sat Sep 12 18:22:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_22362.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_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_22362/09_2026/7jk5_22362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_22362.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_22362.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_22362.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_22362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jk5_22362/09_2026/7jk5_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.37, per 1000 atoms: 0.19 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: 1.43 Conformation dependent library (CDL) restraints added in 723.2 milliseconds 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: 2.02 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: 3.52 Time building geometry restraints manager: 1.88 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: 24250 4.68 - 9.36: 163 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: 8931 17.81 - 35.62: 1139 35.62 - 53.43: 433 53.43 - 71.24: 125 71.24 - 89.05: 24 Dihedral angle restraints: 10652 sinusoidal: 4778 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 10649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1871 0.052 - 0.104: 758 0.104 - 0.155: 141 0.155 - 0.207: 32 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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= 0.413 Angle : 1.140 23.391 24425 Z= 0.765 Chirality : 0.057 0.259 2811 Planarity : 0.007 0.071 2871 Dihedral : 19.120 89.048 6818 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 are 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/Z covalent geometry : bond 0.00717 / 0.41 (17856) covalent geometry : angle 1.14040 / 0.77 (24425) hydrogen bonds : bond 0.14145 / 9.65 ( 911) hydrogen bonds : angle 6.79023 / 4.76 ( 2577) Misc. bond : bond 0.00271 / 0.14 ( 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 : 0.642 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: 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: 0.8683 (mt-10) outliers start: 5 outliers final: 1 residues processed: 304 average time/residue: 0.1395 time to fit residues: 63.0450 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 : 0.641 ------------------------------------------------------------------------------- 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: 30.0000 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... B 348 ASN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 HIS C 58 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 204 GLN C 221 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 HIS C 591 HIS C 715 HIS D 35 ASN D 242 GLN D 274 GLN D 399 HIS E 202 GLN E 278 HIS ** 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 = 0.3430 r_free = 0.3430 target = 0.062808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045228 restraints weight = 88464.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046637 restraints weight = 49767.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.047623 restraints weight = 33565.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.048308 restraints weight = 25330.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.048726 restraints weight = 20694.861| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1859 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= 0.158 Angle : 0.750 9.503 24425 Z= 0.396 Chirality : 0.047 0.345 2811 Planarity : 0.005 0.051 2871 Dihedral : 19.595 80.170 2912 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.06 % Allowed : 13.19 % Favored : 84.75 % 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 are not related in a simple way. whole: -1.20 (0.17), residues: 1961 helix: -0.70 (0.13), residues: 1199 sheet: -2.70 (0.33), residues: 169 loop : 0.12 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 370 TYR 0.021 0.002 TYR C 255 PHE 0.016 0.002 PHE C 362 TRP 0.024 0.002 TRP C 191 HIS 0.009 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (17856) covalent geometry : angle 0.75038 / 0.40 (24425) hydrogen bonds : bond 0.04811 / 3.20 ( 911) hydrogen bonds : angle 5.10259 / 3.57 ( 2577) Misc. bond : bond 0.00203 / 0.11 ( 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 234 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 0.690 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 334 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9305 (pt0) REVERT: B 335 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8935 (mp0) REVERT: B 342 LYS cc_start: 0.9469 (tttm) cc_final: 0.9073 (ptpp) REVERT: B 343 TRP cc_start: 0.9206 (m-10) cc_final: 0.8709 (m100) REVERT: B 421 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 483 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8382 (m-10) REVERT: B 493 MET cc_start: 0.7988 (mmt) cc_final: 0.7085 (tmm) REVERT: C 132 LEU cc_start: 0.9328 (tp) cc_final: 0.9118 (tp) REVERT: C 208 ILE cc_start: 0.9611 (mt) cc_final: 0.9363 (tp) REVERT: C 323 MET cc_start: 0.9248 (tmm) cc_final: 0.8975 (tmm) REVERT: C 340 LYS cc_start: 0.9740 (tptp) cc_final: 0.9475 (tptp) REVERT: C 395 ASP cc_start: 0.9158 (t70) cc_final: 0.8821 (p0) REVERT: C 443 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9253 (tt0) REVERT: C 658 MET cc_start: 0.9077 (tpt) cc_final: 0.8852 (tpp) REVERT: D 46 MET cc_start: 0.9244 (mpp) cc_final: 0.9026 (mpp) REVERT: D 335 ASP cc_start: 0.8842 (m-30) cc_final: 0.8394 (p0) REVERT: D 426 MET cc_start: 0.9247 (mmm) cc_final: 0.8971 (mmm) REVERT: E 69 LEU cc_start: 0.9097 (tp) cc_final: 0.8891 (tp) REVERT: E 164 GLU cc_start: 0.8838 (mp0) cc_final: 0.8393 (mp0) REVERT: E 237 PHE cc_start: 0.8550 (m-10) cc_final: 0.8007 (m-10) REVERT: A 524 MET cc_start: 0.8233 (ptt) cc_final: 0.8024 (tpt) REVERT: A 588 ASP cc_start: 0.8585 (m-30) cc_final: 0.8133 (p0) REVERT: A 790 CYS cc_start: 0.9588 (m) cc_final: 0.9376 (m) REVERT: A 795 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8786 (mt-10) outliers start: 36 outliers final: 18 residues processed: 220 average time/residue: 0.1315 time to fit residues: 44.1368 Evaluate side-chains 182 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 292 LEU 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 840 ILE 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: 2.9990 chunk 52 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 112 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 363 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 HIS C 570 GLN C 585 GLN D 437 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044428 restraints weight = 86716.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.045825 restraints weight = 48774.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.046769 restraints weight = 32815.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.047437 restraints weight = 24650.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.047865 restraints weight = 19997.826| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2335 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= 0.138 Angle : 0.703 9.854 24425 Z= 0.364 Chirality : 0.045 0.285 2811 Planarity : 0.004 0.058 2871 Dihedral : 19.446 78.911 2910 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.34 % Allowed : 14.51 % Favored : 83.15 % 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 are not related in a simple way. whole: -0.44 (0.18), residues: 1961 helix: 0.09 (0.14), residues: 1195 sheet: -2.74 (0.33), residues: 177 loop : 0.15 (0.26), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 419 TYR 0.018 0.001 TYR A 579 PHE 0.021 0.001 PHE C 362 TRP 0.020 0.002 TRP C 191 HIS 0.006 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (17856) covalent geometry : angle 0.70294 / 0.36 (24425) hydrogen bonds : bond 0.04202 / 2.79 ( 911) hydrogen bonds : angle 4.72839 / 3.31 ( 2577) Misc. bond : bond 0.00057 / 0.03 ( 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 222 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8858 (mp0) REVERT: B 342 LYS cc_start: 0.9437 (tttm) cc_final: 0.9030 (ptpp) REVERT: B 343 TRP cc_start: 0.9208 (m-10) cc_final: 0.8709 (m100) REVERT: B 438 ASP cc_start: 0.8054 (p0) cc_final: 0.7803 (p0) REVERT: B 443 ARG cc_start: 0.8999 (mtt90) cc_final: 0.8742 (mmt90) REVERT: B 479 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8933 (ptpp) REVERT: B 483 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8350 (m-10) REVERT: B 493 MET cc_start: 0.8053 (mmt) cc_final: 0.7191 (tmm) REVERT: C 132 LEU cc_start: 0.9264 (tp) cc_final: 0.8992 (tp) REVERT: C 208 ILE cc_start: 0.9613 (mt) cc_final: 0.9342 (tp) REVERT: C 323 MET cc_start: 0.9229 (tmm) cc_final: 0.8957 (tmm) REVERT: C 340 LYS cc_start: 0.9739 (tptp) cc_final: 0.9477 (tptp) REVERT: C 658 MET cc_start: 0.8913 (tpt) cc_final: 0.8595 (tpt) REVERT: D 335 ASP cc_start: 0.8873 (m-30) cc_final: 0.8443 (p0) REVERT: D 426 MET cc_start: 0.9229 (mmm) cc_final: 0.8821 (mmm) REVERT: E 164 GLU cc_start: 0.8883 (mp0) cc_final: 0.8322 (mp0) REVERT: E 237 PHE cc_start: 0.8551 (m-10) cc_final: 0.7943 (m-10) REVERT: A 524 MET cc_start: 0.8418 (ptt) cc_final: 0.8124 (tpp) REVERT: A 588 ASP cc_start: 0.8550 (m-30) cc_final: 0.8173 (p0) REVERT: A 795 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8709 (mt-10) REVERT: A 828 ASN cc_start: 0.9252 (t0) cc_final: 0.8970 (t0) outliers start: 41 outliers final: 17 residues processed: 208 average time/residue: 0.1068 time to fit residues: 35.3711 Evaluate side-chains 180 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 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 253 LEU 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 E residue 22 LEU Chi-restraints excluded: chain E residue 334 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 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: 2.9990 chunk 88 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN D 200 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.043365 restraints weight = 89105.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.044679 restraints weight = 50346.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045600 restraints weight = 34210.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046202 restraints weight = 26001.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046604 restraints weight = 21485.137| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17857 Z= 0.202 Angle : 0.717 12.153 24425 Z= 0.371 Chirality : 0.044 0.349 2811 Planarity : 0.004 0.050 2871 Dihedral : 19.453 80.114 2910 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.40 % Allowed : 15.65 % Favored : 81.95 % 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 are not related in a simple way. whole: 0.05 (0.19), residues: 1961 helix: 0.55 (0.15), residues: 1197 sheet: -2.67 (0.34), residues: 177 loop : 0.19 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 201 TYR 0.019 0.001 TYR A 698 PHE 0.019 0.002 PHE C 362 TRP 0.020 0.002 TRP C 57 HIS 0.006 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (17856) covalent geometry : angle 0.71689 / 0.37 (24425) hydrogen bonds : bond 0.04399 / 2.86 ( 911) hydrogen bonds : angle 4.65506 / 3.25 ( 2577) Misc. bond : bond 0.00072 / 0.04 ( 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 207 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 335 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8911 (mp0) REVERT: B 342 LYS cc_start: 0.9438 (tttm) cc_final: 0.9040 (ptpp) REVERT: B 343 TRP cc_start: 0.9258 (m-10) cc_final: 0.8704 (m100) REVERT: B 443 ARG cc_start: 0.9021 (mtt90) cc_final: 0.8796 (mmt90) REVERT: B 479 LYS cc_start: 0.9252 (ptpp) cc_final: 0.9009 (ptpp) REVERT: B 483 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8404 (m-10) REVERT: B 493 MET cc_start: 0.8155 (mmt) cc_final: 0.7313 (tmm) REVERT: C 132 LEU cc_start: 0.9293 (tp) cc_final: 0.8953 (tp) REVERT: C 208 ILE cc_start: 0.9593 (mt) cc_final: 0.9319 (tp) REVERT: C 323 MET cc_start: 0.9231 (tmm) cc_final: 0.8952 (tmm) REVERT: C 340 LYS cc_start: 0.9744 (tptp) cc_final: 0.9390 (tptp) REVERT: C 395 ASP cc_start: 0.9166 (t70) cc_final: 0.8786 (p0) REVERT: C 450 MET cc_start: 0.9221 (mmt) cc_final: 0.8912 (mtm) REVERT: C 658 MET cc_start: 0.8894 (tpt) cc_final: 0.8648 (tpt) REVERT: D 74 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9110 (mm) REVERT: D 335 ASP cc_start: 0.8889 (m-30) cc_final: 0.8532 (p0) REVERT: D 347 GLU cc_start: 0.8763 (mp0) cc_final: 0.8518 (mp0) REVERT: D 407 MET cc_start: 0.8413 (ptp) cc_final: 0.8170 (mpp) REVERT: D 426 MET cc_start: 0.9271 (mmm) cc_final: 0.8784 (mmm) REVERT: E 143 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9458 (mm) REVERT: E 237 PHE cc_start: 0.8607 (m-10) cc_final: 0.8064 (m-10) REVERT: A 524 MET cc_start: 0.8504 (ptt) cc_final: 0.8269 (tpt) REVERT: A 588 ASP cc_start: 0.8597 (m-30) cc_final: 0.8173 (p0) REVERT: A 750 LEU cc_start: 0.9518 (mt) cc_final: 0.8659 (tp) REVERT: A 790 CYS cc_start: 0.9609 (m) cc_final: 0.9397 (m) REVERT: A 795 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8616 (mp0) REVERT: A 828 ASN cc_start: 0.9272 (t0) cc_final: 0.9035 (t0) outliers start: 42 outliers final: 25 residues processed: 191 average time/residue: 0.1231 time to fit residues: 37.2538 Evaluate side-chains 186 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 478 ILE 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 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 334 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 17 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 201 optimal weight: 50.0000 chunk 95 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 363 GLN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.061829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.044381 restraints weight = 87955.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.045759 restraints weight = 49933.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046705 restraints weight = 33836.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.047288 restraints weight = 25644.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.047748 restraints weight = 21317.757| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17857 Z= 0.123 Angle : 0.660 10.356 24425 Z= 0.341 Chirality : 0.043 0.288 2811 Planarity : 0.004 0.051 2871 Dihedral : 19.372 78.706 2910 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.00 % Allowed : 16.90 % Favored : 81.10 % 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 are not related in a simple way. whole: 0.23 (0.19), residues: 1961 helix: 0.71 (0.15), residues: 1201 sheet: -2.54 (0.34), residues: 177 loop : 0.20 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.021 0.001 TYR A 579 PHE 0.020 0.001 PHE C 362 TRP 0.015 0.001 TRP C 57 HIS 0.006 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (17856) covalent geometry : angle 0.65971 / 0.34 (24425) hydrogen bonds : bond 0.03783 / 2.49 ( 911) hydrogen bonds : angle 4.44257 / 3.11 ( 2577) Misc. bond : bond 0.00042 / 0.02 ( 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 204 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 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: 0.9423 (tttm) cc_final: 0.9031 (mtmm) REVERT: B 343 TRP cc_start: 0.9153 (m-10) cc_final: 0.8678 (m100) REVERT: B 441 MET cc_start: 0.8798 (mtp) cc_final: 0.8528 (pmm) REVERT: B 479 LYS cc_start: 0.9268 (ptpp) cc_final: 0.9044 (ptpp) REVERT: B 483 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8298 (m-10) REVERT: B 493 MET cc_start: 0.8360 (mmt) cc_final: 0.7199 (tmm) REVERT: C 132 LEU cc_start: 0.9220 (tp) cc_final: 0.8880 (tp) REVERT: C 208 ILE cc_start: 0.9570 (mt) cc_final: 0.9353 (tp) REVERT: C 323 MET cc_start: 0.9208 (tmm) cc_final: 0.8937 (tmm) REVERT: D 335 ASP cc_start: 0.8785 (m-30) cc_final: 0.8413 (p0) REVERT: D 407 MET cc_start: 0.8299 (ptp) cc_final: 0.7967 (mpp) REVERT: D 426 MET cc_start: 0.9228 (mmm) cc_final: 0.8787 (mmm) REVERT: E 143 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9440 (mm) REVERT: E 237 PHE cc_start: 0.8516 (m-10) cc_final: 0.8027 (m-10) REVERT: A 524 MET cc_start: 0.8487 (ptt) cc_final: 0.8215 (tpp) REVERT: A 588 ASP cc_start: 0.8572 (m-30) cc_final: 0.8173 (p0) REVERT: A 630 LEU cc_start: 0.9076 (tp) cc_final: 0.8818 (tp) REVERT: A 750 LEU cc_start: 0.9503 (mt) cc_final: 0.8674 (tp) REVERT: A 790 CYS cc_start: 0.9604 (m) cc_final: 0.9355 (m) REVERT: A 828 ASN cc_start: 0.9197 (t0) cc_final: 0.8933 (t0) outliers start: 35 outliers final: 19 residues processed: 195 average time/residue: 0.1223 time to fit residues: 37.6013 Evaluate side-chains 173 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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 81 ASP 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 451 LEU 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 74 LEU 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 564 VAL 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: 5.9990 chunk 176 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 chunk 199 optimal weight: 50.0000 chunk 186 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 477 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 = 0.3374 r_free = 0.3374 target = 0.059965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.042934 restraints weight = 89595.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.044255 restraints weight = 51096.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.045189 restraints weight = 34803.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045820 restraints weight = 26442.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.046236 restraints weight = 21770.673| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17857 Z= 0.204 Angle : 0.686 9.063 24425 Z= 0.357 Chirality : 0.043 0.345 2811 Planarity : 0.004 0.053 2871 Dihedral : 19.363 80.694 2910 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.23 % Allowed : 17.76 % Favored : 80.01 % 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 are not related in a simple way. whole: 0.44 (0.19), residues: 1961 helix: 0.90 (0.15), residues: 1194 sheet: -2.48 (0.36), residues: 171 loop : 0.21 (0.28), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 573 TYR 0.020 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.023 0.002 TRP C 57 HIS 0.012 0.001 HIS C 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (17856) covalent geometry : angle 0.68581 / 0.36 (24425) hydrogen bonds : bond 0.04230 / 2.74 ( 911) hydrogen bonds : angle 4.51472 / 3.15 ( 2577) Misc. bond : bond 0.00081 / 0.04 ( 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 195 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.742 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: 0.9055 (mtmm) REVERT: B 343 TRP cc_start: 0.9223 (m-10) cc_final: 0.8714 (m100) REVERT: B 441 MET cc_start: 0.8895 (mtp) cc_final: 0.8568 (pmm) REVERT: B 479 LYS cc_start: 0.9276 (ptpp) cc_final: 0.9055 (ptpp) REVERT: B 483 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8344 (m-10) REVERT: B 493 MET cc_start: 0.8392 (mmt) cc_final: 0.7197 (tmm) REVERT: C 132 LEU cc_start: 0.9273 (tp) cc_final: 0.8909 (tp) REVERT: C 208 ILE cc_start: 0.9582 (mt) cc_final: 0.9326 (tp) REVERT: C 323 MET cc_start: 0.9212 (tmm) cc_final: 0.8929 (tmm) REVERT: D 335 ASP cc_start: 0.8879 (m-30) cc_final: 0.8484 (p0) REVERT: D 347 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8458 (mm-30) REVERT: D 426 MET cc_start: 0.9290 (mmm) cc_final: 0.8755 (mmm) REVERT: E 143 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9447 (mm) REVERT: E 237 PHE cc_start: 0.8606 (m-10) cc_final: 0.8110 (m-10) REVERT: A 524 MET cc_start: 0.8486 (ptt) cc_final: 0.8275 (tpt) REVERT: A 588 ASP cc_start: 0.8627 (m-30) cc_final: 0.8178 (p0) REVERT: A 630 LEU cc_start: 0.9104 (tp) cc_final: 0.8878 (tp) REVERT: A 750 LEU cc_start: 0.9512 (mt) cc_final: 0.8623 (tt) REVERT: A 790 CYS cc_start: 0.9639 (m) cc_final: 0.9411 (m) REVERT: A 828 ASN cc_start: 0.9228 (t0) cc_final: 0.8996 (t0) outliers start: 39 outliers final: 23 residues processed: 184 average time/residue: 0.1188 time to fit residues: 35.1293 Evaluate side-chains 176 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 81 ASP 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 292 LEU Chi-restraints excluded: chain C residue 451 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 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 388 VAL 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 E residue 444 ILE Chi-restraints excluded: chain A residue 564 VAL 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: 5.9990 chunk 82 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.0470 chunk 85 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 477 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 = 0.3412 r_free = 0.3412 target = 0.061193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.043890 restraints weight = 87873.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.045262 restraints weight = 49388.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.046225 restraints weight = 33341.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.046868 restraints weight = 25268.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.047268 restraints weight = 20748.713| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17857 Z= 0.122 Angle : 0.674 11.944 24425 Z= 0.341 Chirality : 0.043 0.408 2811 Planarity : 0.004 0.053 2871 Dihedral : 19.311 79.374 2910 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.71 % Allowed : 18.62 % Favored : 79.67 % 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 are not related in a simple way. whole: 0.51 (0.19), residues: 1961 helix: 0.95 (0.15), residues: 1198 sheet: -2.39 (0.37), residues: 169 loop : 0.20 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 337 TYR 0.022 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.021 0.001 TRP C 57 HIS 0.005 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17856) covalent geometry : angle 0.67407 / 0.34 (24425) hydrogen bonds : bond 0.03675 / 2.42 ( 911) hydrogen bonds : angle 4.38563 / 3.06 ( 2577) Misc. bond : bond 0.00023 / 0.01 ( 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 195 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.654 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: 0.9443 (tttm) cc_final: 0.9053 (mtmm) REVERT: B 343 TRP cc_start: 0.9133 (m-10) cc_final: 0.8656 (m100) REVERT: B 403 ASP cc_start: 0.9239 (m-30) cc_final: 0.8946 (p0) REVERT: B 441 MET cc_start: 0.8930 (mtp) cc_final: 0.8637 (pmm) REVERT: B 479 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9050 (ptpp) REVERT: B 483 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8251 (m-10) REVERT: B 493 MET cc_start: 0.8371 (mmt) cc_final: 0.7065 (tmm) REVERT: C 132 LEU cc_start: 0.9222 (tp) cc_final: 0.8858 (tp) REVERT: C 208 ILE cc_start: 0.9567 (mt) cc_final: 0.9300 (tp) REVERT: C 323 MET cc_start: 0.9196 (tmm) cc_final: 0.8929 (tmm) REVERT: D 335 ASP cc_start: 0.8826 (m-30) cc_final: 0.8452 (p0) REVERT: D 347 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8481 (mm-30) REVERT: D 407 MET cc_start: 0.8205 (mtm) cc_final: 0.7669 (mpp) REVERT: D 426 MET cc_start: 0.9242 (mmm) cc_final: 0.8754 (mmm) REVERT: E 175 ILE cc_start: 0.9504 (tt) cc_final: 0.9089 (mt) REVERT: E 237 PHE cc_start: 0.8474 (m-10) cc_final: 0.7975 (m-10) REVERT: A 588 ASP cc_start: 0.8577 (m-30) cc_final: 0.8154 (p0) REVERT: A 750 LEU cc_start: 0.9483 (mt) cc_final: 0.8696 (tp) REVERT: A 790 CYS cc_start: 0.9642 (m) cc_final: 0.9380 (m) REVERT: A 828 ASN cc_start: 0.9178 (t0) cc_final: 0.8936 (t0) REVERT: A 832 MET cc_start: 0.9190 (mmp) cc_final: 0.8900 (mmm) outliers start: 30 outliers final: 19 residues processed: 189 average time/residue: 0.1154 time to fit residues: 34.9804 Evaluate side-chains 176 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL 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 74 LEU 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 A residue 564 VAL 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: 0.7980 chunk 53 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 176 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 203 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 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 = 0.060670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043425 restraints weight = 89439.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.044798 restraints weight = 50535.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.045756 restraints weight = 34293.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.046339 restraints weight = 26016.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046787 restraints weight = 21542.361| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17857 Z= 0.137 Angle : 0.689 12.480 24425 Z= 0.346 Chirality : 0.043 0.359 2811 Planarity : 0.004 0.053 2871 Dihedral : 19.242 80.663 2910 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.83 % Allowed : 19.13 % Favored : 79.04 % 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 are not related in a simple way. whole: 0.59 (0.19), residues: 1961 helix: 1.02 (0.15), residues: 1199 sheet: -2.28 (0.39), residues: 160 loop : 0.14 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.024 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.031 0.001 TRP C 57 HIS 0.005 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (17856) covalent geometry : angle 0.68923 / 0.35 (24425) hydrogen bonds : bond 0.03733 / 2.43 ( 911) hydrogen bonds : angle 4.38747 / 3.06 ( 2577) Misc. bond : bond 0.00042 / 0.02 ( 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 194 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.628 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: 0.9456 (tttm) cc_final: 0.9038 (mtmm) REVERT: B 343 TRP cc_start: 0.9161 (m-10) cc_final: 0.8650 (m100) REVERT: B 403 ASP cc_start: 0.9233 (m-30) cc_final: 0.8941 (p0) REVERT: B 441 MET cc_start: 0.8912 (mtp) cc_final: 0.8620 (pmm) REVERT: B 479 LYS cc_start: 0.9254 (ptpp) cc_final: 0.9035 (ptpp) REVERT: B 483 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8236 (m-10) REVERT: C 132 LEU cc_start: 0.9253 (tp) cc_final: 0.8889 (tp) REVERT: C 208 ILE cc_start: 0.9567 (mt) cc_final: 0.9313 (tp) REVERT: C 222 ASP cc_start: 0.9110 (p0) cc_final: 0.8844 (p0) REVERT: C 323 MET cc_start: 0.9189 (tmm) cc_final: 0.8896 (tmm) REVERT: D 53 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9293 (mt) REVERT: D 335 ASP cc_start: 0.8830 (m-30) cc_final: 0.8485 (p0) REVERT: D 407 MET cc_start: 0.8228 (mtm) cc_final: 0.7725 (mpp) REVERT: D 426 MET cc_start: 0.9250 (mmm) cc_final: 0.8740 (mmm) REVERT: E 237 PHE cc_start: 0.8454 (m-10) cc_final: 0.7974 (m-10) REVERT: A 588 ASP cc_start: 0.8577 (m-30) cc_final: 0.8165 (p0) REVERT: A 750 LEU cc_start: 0.9466 (mt) cc_final: 0.8585 (tt) REVERT: A 790 CYS cc_start: 0.9642 (m) cc_final: 0.9431 (m) REVERT: A 828 ASN cc_start: 0.9161 (t0) cc_final: 0.8936 (t0) outliers start: 32 outliers final: 22 residues processed: 187 average time/residue: 0.1170 time to fit residues: 34.8655 Evaluate side-chains 179 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 140 LEU 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 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 74 LEU 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 419 VAL Chi-restraints excluded: chain A residue 564 VAL 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: 0.9990 chunk 111 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 202 optimal weight: 50.0000 chunk 194 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.060307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.043175 restraints weight = 88763.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.044518 restraints weight = 50038.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.045458 restraints weight = 33858.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046035 restraints weight = 25660.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046471 restraints weight = 21297.349| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17857 Z= 0.159 Angle : 0.705 13.099 24425 Z= 0.354 Chirality : 0.044 0.417 2811 Planarity : 0.004 0.053 2871 Dihedral : 19.229 80.901 2910 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.60 % Allowed : 19.47 % Favored : 78.93 % 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 are not related in a simple way. whole: 0.63 (0.20), residues: 1961 helix: 1.06 (0.15), residues: 1201 sheet: -2.25 (0.39), residues: 160 loop : 0.12 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.022 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.027 0.002 TRP C 57 HIS 0.006 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (17856) covalent geometry : angle 0.70529 / 0.35 (24425) hydrogen bonds : bond 0.03870 / 2.48 ( 911) hydrogen bonds : angle 4.42056 / 3.07 ( 2577) Misc. bond : bond 0.00057 / 0.03 ( 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 181 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.585 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 342 LYS cc_start: 0.9445 (tttm) cc_final: 0.9028 (mtmm) REVERT: B 343 TRP cc_start: 0.9156 (m-10) cc_final: 0.8626 (m100) REVERT: B 349 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 441 MET cc_start: 0.8890 (mtp) cc_final: 0.8636 (pmm) REVERT: C 132 LEU cc_start: 0.9261 (tp) cc_final: 0.8916 (tp) REVERT: C 208 ILE cc_start: 0.9566 (mt) cc_final: 0.9312 (tp) REVERT: C 222 ASP cc_start: 0.9134 (p0) cc_final: 0.8842 (p0) REVERT: C 323 MET cc_start: 0.9196 (tmm) cc_final: 0.8910 (tmm) REVERT: D 53 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9299 (mt) REVERT: D 239 TYR cc_start: 0.8988 (m-10) cc_final: 0.8751 (m-10) REVERT: D 335 ASP cc_start: 0.8853 (m-30) cc_final: 0.8510 (p0) REVERT: D 407 MET cc_start: 0.8254 (mtm) cc_final: 0.7739 (mpp) REVERT: D 426 MET cc_start: 0.9272 (mmm) cc_final: 0.8785 (mmm) REVERT: E 237 PHE cc_start: 0.8504 (m-80) cc_final: 0.8039 (m-10) REVERT: A 588 ASP cc_start: 0.8596 (m-30) cc_final: 0.8161 (p0) REVERT: A 750 LEU cc_start: 0.9463 (mt) cc_final: 0.8611 (tt) REVERT: A 790 CYS cc_start: 0.9644 (m) cc_final: 0.9397 (m) outliers start: 28 outliers final: 24 residues processed: 176 average time/residue: 0.1151 time to fit residues: 32.0174 Evaluate side-chains 174 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 140 LEU 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 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 74 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 564 VAL 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: 2.9990 chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 chunk 168 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 ASN ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.060569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.043427 restraints weight = 88128.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044755 restraints weight = 50292.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.045690 restraints weight = 34251.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.046286 restraints weight = 26050.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046662 restraints weight = 21556.781| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17857 Z= 0.135 Angle : 0.702 13.477 24425 Z= 0.350 Chirality : 0.043 0.383 2811 Planarity : 0.004 0.054 2871 Dihedral : 19.179 80.637 2910 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.43 % Allowed : 19.82 % Favored : 78.75 % 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 are not related in a simple way. whole: 0.69 (0.20), residues: 1961 helix: 1.14 (0.15), residues: 1191 sheet: -2.15 (0.39), residues: 160 loop : 0.05 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.027 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.024 0.001 TRP C 57 HIS 0.007 0.001 HIS C 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (17856) covalent geometry : angle 0.70198 / 0.35 (24425) hydrogen bonds : bond 0.03645 / 2.35 ( 911) hydrogen bonds : angle 4.36520 / 3.04 ( 2577) Misc. bond : bond 0.00045 / 0.02 ( 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 181 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.599 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 343 TRP cc_start: 0.9107 (m-10) cc_final: 0.8661 (m100) REVERT: B 349 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8555 (mm-30) REVERT: B 441 MET cc_start: 0.8894 (mtp) cc_final: 0.8669 (pmm) REVERT: B 483 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8237 (m-10) REVERT: C 132 LEU cc_start: 0.9218 (tp) cc_final: 0.8874 (tp) REVERT: C 222 ASP cc_start: 0.9126 (p0) cc_final: 0.8826 (p0) REVERT: C 323 MET cc_start: 0.9209 (tmm) cc_final: 0.8933 (tmm) REVERT: D 53 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9294 (mt) REVERT: D 239 TYR cc_start: 0.9007 (m-10) cc_final: 0.8773 (m-10) REVERT: D 335 ASP cc_start: 0.8849 (m-30) cc_final: 0.8490 (p0) REVERT: D 407 MET cc_start: 0.8260 (mtm) cc_final: 0.7735 (mpp) REVERT: D 426 MET cc_start: 0.9274 (mmm) cc_final: 0.8740 (mmm) REVERT: E 237 PHE cc_start: 0.8485 (m-80) cc_final: 0.8012 (m-10) REVERT: E 413 LEU cc_start: 0.9680 (mp) cc_final: 0.9377 (mt) REVERT: A 588 ASP cc_start: 0.8615 (m-30) cc_final: 0.8226 (p0) REVERT: A 750 LEU cc_start: 0.9465 (mt) cc_final: 0.8616 (tt) REVERT: A 790 CYS cc_start: 0.9661 (m) cc_final: 0.9410 (m) outliers start: 25 outliers final: 23 residues processed: 178 average time/residue: 0.1143 time to fit residues: 32.2817 Evaluate side-chains 176 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 140 LEU 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 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 74 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 277 ARG Chi-restraints excluded: chain E residue 345 ARG Chi-restraints excluded: chain E residue 419 VAL 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: 2.9990 chunk 194 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 151 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 412 HIS ** 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 = 0.3401 r_free = 0.3401 target = 0.060387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.043270 restraints weight = 88815.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.044609 restraints weight = 50632.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.045477 restraints weight = 34382.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046113 restraints weight = 26410.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.046509 restraints weight = 21785.894| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17857 Z= 0.143 Angle : 0.701 13.918 24425 Z= 0.348 Chirality : 0.043 0.352 2811 Planarity : 0.004 0.054 2871 Dihedral : 19.111 81.248 2910 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.54 % Allowed : 19.70 % Favored : 78.75 % 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 are not related in a simple way. whole: 0.78 (0.20), residues: 1961 helix: 1.23 (0.15), residues: 1190 sheet: -2.13 (0.39), residues: 161 loop : 0.07 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 443 TYR 0.026 0.001 TYR A 579 PHE 0.019 0.001 PHE C 362 TRP 0.020 0.001 TRP C 57 HIS 0.006 0.001 HIS A 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17856) covalent geometry : angle 0.70062 / 0.35 (24425) hydrogen bonds : bond 0.03670 / 2.35 ( 911) hydrogen bonds : angle 4.33144 / 3.01 ( 2577) Misc. bond : bond 0.00050 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3000.21 seconds wall clock time: 52 minutes 43.24 seconds (3163.24 seconds total)