Starting phenix.real_space_refine on Mon Oct 26 17:09:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgr_22329/10_2026/7jgr_22329.map" } 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 80 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 13572 2.51 5 N 3813 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21717 Number of models: 1 Model: "" Number of chains: 13 Chain: "B" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2321 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 3 Chain: "C" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4918 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 588} Chain breaks: 7 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: 3161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3161 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3129 Classifications: {'peptide': 401} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 383} Chain: "G" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2974 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain breaks: 2 Chain: "H" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 693 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 701 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.22, per 1000 atoms: 0.19 Number of scatterers: 21717 At special positions: 0 Unit cell: (122.98, 159.1, 123.84, 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 111 16.00 P 80 15.00 Mg 4 11.99 O 4137 8.00 N 3813 7.00 C 13572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 773.8 milliseconds 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4844 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 13 sheets defined 64.7% alpha, 7.2% beta 28 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 361 through 372 Processing helix chain 'B' and resid 389 through 401 Processing helix chain 'B' and resid 410 through 424 Processing helix chain 'B' and resid 444 through 456 removed outlier: 3.601A pdb=" N GLN B 448 " --> pdb=" O ASN B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 476 through 483 Processing helix chain 'B' and resid 516 through 524 Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 555 through 565 Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.661A pdb=" N LEU B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.525A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 89 removed outlier: 5.136A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 109 Processing helix chain 'C' and resid 110 through 124 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 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.635A pdb=" N PHE C 215 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 230 Processing helix chain 'C' and resid 245 through 253 removed outlier: 3.850A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 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 removed outlier: 3.689A pdb=" N PHE C 314 " --> pdb=" O SER C 310 " (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 Processing helix chain 'C' and resid 373 through 380 Processing helix chain 'C' and resid 382 through 416 Proline residue: C 390 - end of helix removed outlier: 4.666A pdb=" N GLU C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C 413 " --> pdb=" O PHE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.801A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 436 " --> pdb=" O ASN C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 453 removed outlier: 3.631A 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 508 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 563 through 576 removed outlier: 3.680A pdb=" N LYS C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 590 through 593 removed outlier: 3.792A pdb=" N LEU C 593 " --> pdb=" O ILE C 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 590 through 593' Processing helix chain 'C' and resid 598 through 607 removed outlier: 4.247A pdb=" N VAL C 602 " --> pdb=" O ASP C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.535A pdb=" N ALA C 613 " --> pdb=" O ALA C 609 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN C 620 " --> pdb=" O THR C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 626 Processing helix chain 'C' and resid 643 through 654 removed outlier: 3.545A pdb=" N VAL C 647 " --> pdb=" O PRO C 643 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 672 Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'D' and resid 3 through 21 removed outlier: 3.742A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.573A pdb=" N GLY D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 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 95 through 107 Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 148 through 153 removed outlier: 3.570A pdb=" N PHE D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 157 removed outlier: 6.292A pdb=" N ASN D 157 " --> pdb=" O ALA D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 157' Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.835A pdb=" N SER D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 211 through 224 removed outlier: 3.532A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 244 removed outlier: 4.255A pdb=" N ILE D 244 " --> pdb=" O ASN D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 4.118A pdb=" N ARG D 253 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 255 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 261 removed outlier: 3.637A pdb=" N GLU D 260 " --> pdb=" O ASP D 257 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 257 through 261' Processing helix chain 'D' and resid 264 through 280 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 297 through 310 removed outlier: 3.514A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 333 removed outlier: 3.719A pdb=" N GLY D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 344 through 362 Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.723A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 403 removed outlier: 3.653A pdb=" N ALA D 403 " --> pdb=" O HIS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 removed outlier: 3.583A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 removed outlier: 3.819A pdb=" N GLN D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) 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 76 through 89 removed outlier: 3.836A pdb=" N MET E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.599A pdb=" N ALA E 95 " --> pdb=" O GLN E 92 " (cutoff:3.500A) removed outlier: 3.746A 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 127 through 134 removed outlier: 3.754A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 134 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.726A pdb=" N VAL E 141 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 193 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 212 through 219 Processing helix chain 'E' and resid 222 through 238 removed outlier: 4.106A pdb=" N VAL E 236 " --> pdb=" O LEU E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 4.300A 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: 3.584A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 290 No H-bonds generated for 'chain 'E' and resid 288 through 290' Processing helix chain 'E' and resid 322 through 338 Processing helix chain 'E' and resid 342 through 348 removed outlier: 4.040A pdb=" N VAL E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 394 removed outlier: 4.181A pdb=" N GLU E 394 " --> pdb=" O TYR E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 removed outlier: 4.013A pdb=" N LEU E 404 " --> pdb=" O THR E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 449 removed outlier: 3.659A pdb=" N VAL E 441 " --> pdb=" O GLY E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 456 removed outlier: 3.572A pdb=" N GLN E 454 " --> pdb=" O ASN E 451 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 456 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 238 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 545 through 549 Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 571 through 588 Processing helix chain 'A' and resid 603 through 621 removed outlier: 3.535A pdb=" N THR A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 621 " --> pdb=" O ARG A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 652 removed outlier: 4.039A pdb=" N VAL A 645 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 3.614A 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 685 through 690 removed outlier: 3.747A pdb=" N CYS A 690 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 703 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 765 through 778 removed outlier: 3.608A pdb=" N ALA A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 800 removed outlier: 4.077A pdb=" N ALA A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 791 " --> pdb=" O LEU A 787 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 818 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 830 through 848 removed outlier: 3.652A 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 removed outlier: 3.823A pdb=" N ARG A 880 " --> pdb=" O GLY A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 918 removed outlier: 3.672A pdb=" N ILE A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 260 removed outlier: 4.027A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 287 Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 313 through 319 Processing helix chain 'G' and resid 332 through 334 No H-bonds generated for 'chain 'G' and resid 332 through 334' Processing helix chain 'G' and resid 335 through 345 Processing helix chain 'G' and resid 352 through 366 removed outlier: 3.866A pdb=" N THR G 366 " --> pdb=" O ARG G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 382 removed outlier: 3.535A pdb=" N GLN G 380 " --> pdb=" O GLU G 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 394 Processing helix chain 'G' and resid 413 through 419 Processing helix chain 'G' and resid 420 through 425 removed outlier: 3.631A pdb=" N ALA G 424 " --> pdb=" O ARG G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 454 removed outlier: 3.616A pdb=" N ALA G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA G 454 " --> pdb=" O ARG G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 456 through 460 removed outlier: 3.863A pdb=" N VAL G 459 " --> pdb=" O VAL G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 476 removed outlier: 3.670A pdb=" N ALA G 470 " --> pdb=" O GLN G 466 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 474 " --> pdb=" O ALA G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 498 removed outlier: 3.703A pdb=" N ALA G 482 " --> pdb=" O ASP G 478 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL G 490 " --> pdb=" O GLY G 486 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN G 495 " --> pdb=" O GLU G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 542 removed outlier: 3.743A pdb=" N VAL G 534 " --> pdb=" O GLN G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 574 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.795A pdb=" N VAL G 587 " --> pdb=" O ARG G 583 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 590 " --> pdb=" O GLU G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 601 through 614 removed outlier: 4.033A pdb=" N GLY G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR G 614 " --> pdb=" O ASP G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 625 through 628 Processing helix chain 'G' and resid 636 through 645 removed outlier: 3.767A pdb=" N ALA G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER G 645 " --> pdb=" O HIS G 641 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 655 removed outlier: 3.647A pdb=" N SER G 652 " --> pdb=" O GLN G 648 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 655 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 660 removed outlier: 3.600A pdb=" N CYS G 659 " --> pdb=" O ASP G 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 485 through 488 removed outlier: 6.265A pdb=" N ASN B 352 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TRP B 488 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 354 " --> pdb=" O TRP B 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 378 " --> pdb=" O TYR C 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.516A pdb=" N MET B 553 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.794A pdb=" N VAL C 239 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 262 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR C 98 " --> pdb=" O ARG C 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 291 through 292 removed outlier: 7.624A pdb=" N HIS C 291 " --> pdb=" O PHE C 596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 658 through 660 Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 7.250A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) 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 65 through 70 removed outlier: 6.104A pdb=" N ARG E 65 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA E 124 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA E 67 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASP E 126 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 69 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE E 121 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE E 156 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE E 37 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N SER E 159 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU E 39 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 416 through 418 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 633 removed outlier: 6.414A pdb=" N GLY A 592 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR A 715 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET A 594 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ALA A 717 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 596 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N LEU A 740 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR A 595 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE A 742 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N SER A 597 " --> pdb=" O PHE A 742 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 851 through 853 removed outlier: 3.531A pdb=" N THR A 852 " --> pdb=" O ILE A 904 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 320 through 326 removed outlier: 6.953A pdb=" N LEU G 293 " --> pdb=" O GLY G 407 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA G 409 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL G 295 " --> pdb=" O ALA G 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 579 through 580 removed outlier: 4.482A pdb=" N ILE G 579 " --> pdb=" O VAL G 631 " (cutoff:3.500A) 1094 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 3.97 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5636 1.33 - 1.46: 4757 1.46 - 1.58: 11524 1.58 - 1.70: 153 1.70 - 1.82: 163 Bond restraints: 22233 Sorted by residual: bond pdb=" O3' DT I 46 " pdb=" P DA I 47 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.20e-02 6.94e+03 6.59e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.20e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " 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 A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.73e+01 bond pdb=" C4 ATP G 901 " pdb=" C5 ATP G 901 " ideal model delta sigma weight residual 1.388 1.462 -0.074 1.00e-02 1.00e+04 5.51e+01 ... (remaining 22228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 30174 4.24 - 8.48: 152 8.48 - 12.72: 13 12.72 - 16.96: 5 16.96 - 21.20: 5 Bond angle restraints: 30349 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 139.87 118.67 21.20 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 121.08 18.79 1.00e+00 1.00e+00 3.53e+02 angle pdb=" PB ATP G 901 " pdb=" O3B ATP G 901 " pdb=" PG ATP G 901 " ideal model delta sigma weight residual 139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 119.69 17.14 1.00e+00 1.00e+00 2.94e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 122.91 16.96 1.00e+00 1.00e+00 2.88e+02 ... (remaining 30344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11500 17.93 - 35.86: 1243 35.86 - 53.79: 473 53.79 - 71.72: 114 71.72 - 89.64: 24 Dihedral angle restraints: 13354 sinusoidal: 5934 harmonic: 7420 Sorted by residual: dihedral pdb=" CA LEU G 259 " pdb=" C LEU G 259 " pdb=" N ASN G 260 " pdb=" CA ASN G 260 " ideal model delta harmonic sigma weight residual 180.00 150.60 29.40 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA GLN C 347 " pdb=" C GLN C 347 " pdb=" N LEU C 348 " pdb=" CA LEU C 348 " ideal model delta harmonic sigma weight residual -180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA SER G 349 " pdb=" C SER G 349 " pdb=" N GLY G 350 " pdb=" CA GLY G 350 " ideal model delta harmonic sigma weight residual 180.00 156.50 23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 13351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2814 0.063 - 0.126: 586 0.126 - 0.189: 97 0.189 - 0.252: 4 0.252 - 0.315: 2 Chirality restraints: 3503 Sorted by residual: chirality pdb=" CG LEU C 275 " pdb=" CB LEU C 275 " pdb=" CD1 LEU C 275 " pdb=" CD2 LEU C 275 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.31 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C4' DA I 42 " pdb=" C5' DA I 42 " pdb=" O4' DA I 42 " pdb=" C3' DA I 42 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL E 221 " pdb=" CA VAL E 221 " pdb=" CG1 VAL E 221 " pdb=" CG2 VAL E 221 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3500 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 872 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 873 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 873 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 873 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 150 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" CG ASN E 150 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN E 150 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN E 150 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 281 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO E 282 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 282 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 282 " -0.032 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 53 2.42 - 3.04: 10928 3.04 - 3.66: 33489 3.66 - 4.28: 49920 4.28 - 4.90: 82555 Nonbonded interactions: 176945 Sorted by model distance: nonbonded pdb=" O2 DC H 18 " pdb=" N2 DG I 51 " model vdw 1.799 2.496 nonbonded pdb=" N3 DC H 18 " pdb=" N1 DG I 51 " model vdw 2.066 2.560 nonbonded pdb=" OG1 THR G 304 " pdb="MG MG G 902 " model vdw 2.089 2.170 nonbonded pdb=" OG1 THR D 63 " pdb="MG MG D 902 " model vdw 2.114 2.170 nonbonded pdb=" O2B ATP G 901 " pdb="MG MG G 902 " model vdw 2.128 2.170 ... (remaining 176940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 20.410 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.006 0.097 22233 Z= 0.376 Angle : 0.972 21.197 30349 Z= 0.642 Chirality : 0.053 0.315 3503 Planarity : 0.006 0.087 3607 Dihedral : 17.797 89.644 8510 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.36 % Allowed : 5.00 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -2.88 (0.14), residues: 2481 helix: -2.59 (0.08), residues: 1479 sheet: -2.73 (0.28), residues: 233 loop : 0.54 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 480 TYR 0.028 0.002 TYR E 258 PHE 0.026 0.003 PHE C 215 TRP 0.015 0.002 TRP C 191 HIS 0.006 0.001 HIS E 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.38 (22233) covalent geometry : angle 0.97215 / 0.64 (30349) hydrogen bonds : bond 0.15553 / 10.41 ( 1156) hydrogen bonds : angle 6.44275 / 4.55 ( 3312) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 587 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 MET cc_start: 0.9591 (mmm) cc_final: 0.9172 (tpt) REVERT: B 342 LYS cc_start: 0.9469 (tttt) cc_final: 0.9167 (tptp) REVERT: B 388 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9048 (tp) REVERT: B 417 MET cc_start: 0.9355 (ttt) cc_final: 0.9133 (tmm) REVERT: B 488 TRP cc_start: 0.9074 (m100) cc_final: 0.8701 (m100) REVERT: B 585 LYS cc_start: 0.9423 (mttt) cc_final: 0.9196 (tmtt) REVERT: C 45 VAL cc_start: 0.8843 (t) cc_final: 0.8335 (t) REVERT: C 223 LEU cc_start: 0.9720 (tp) cc_final: 0.9494 (pp) REVERT: C 323 MET cc_start: 0.9154 (ttp) cc_final: 0.8885 (tmm) REVERT: C 353 MET cc_start: 0.8390 (mmt) cc_final: 0.7654 (mmt) REVERT: C 362 PHE cc_start: 0.9052 (t80) cc_final: 0.8823 (t80) REVERT: C 383 ASP cc_start: 0.9328 (m-30) cc_final: 0.8975 (p0) REVERT: C 389 LEU cc_start: 0.9132 (mt) cc_final: 0.8754 (mt) REVERT: C 411 THR cc_start: 0.9031 (p) cc_final: 0.8698 (t) REVERT: C 429 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9363 (mt) REVERT: C 433 CYS cc_start: 0.9222 (m) cc_final: 0.8988 (m) REVERT: C 450 MET cc_start: 0.8880 (mtt) cc_final: 0.7789 (mtt) REVERT: C 467 LEU cc_start: 0.9208 (mm) cc_final: 0.8825 (tt) REVERT: C 571 LEU cc_start: 0.9502 (mm) cc_final: 0.9199 (tp) REVERT: C 594 PHE cc_start: 0.9122 (m-80) cc_final: 0.8746 (m-80) REVERT: C 699 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8715 (mt-10) REVERT: C 707 LYS cc_start: 0.8757 (pttp) cc_final: 0.8202 (pptt) REVERT: D 48 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7576 (mt-10) REVERT: D 151 LEU cc_start: 0.9642 (mt) cc_final: 0.9418 (mp) REVERT: D 217 ASP cc_start: 0.9118 (m-30) cc_final: 0.8818 (m-30) REVERT: E 11 LEU cc_start: 0.9589 (mt) cc_final: 0.9342 (tt) REVERT: E 26 ILE cc_start: 0.9532 (pt) cc_final: 0.9328 (pt) REVERT: E 82 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8700 (mt-10) REVERT: E 94 ASP cc_start: 0.8350 (t70) cc_final: 0.7965 (t0) REVERT: E 159 SER cc_start: 0.7990 (t) cc_final: 0.7260 (m) REVERT: E 337 HIS cc_start: 0.8141 (t-90) cc_final: 0.7685 (t-90) REVERT: F 232 MET cc_start: 0.9399 (tpp) cc_final: 0.9141 (mmm) REVERT: A 524 MET cc_start: 0.9451 (mmm) cc_final: 0.9222 (mmp) REVERT: A 526 LYS cc_start: 0.9525 (mttt) cc_final: 0.9250 (mtmt) REVERT: A 648 TYR cc_start: 0.9116 (t80) cc_final: 0.8864 (t80) REVERT: A 695 ASP cc_start: 0.8879 (p0) cc_final: 0.8616 (p0) REVERT: A 788 ASP cc_start: 0.9129 (m-30) cc_final: 0.8655 (m-30) REVERT: A 894 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8306 (mt-10) REVERT: A 911 ASP cc_start: 0.8373 (p0) cc_final: 0.7991 (p0) REVERT: G 327 CYS cc_start: 0.8742 (m) cc_final: 0.8073 (m) REVERT: G 368 LYS cc_start: 0.8870 (mptt) cc_final: 0.8609 (tppt) REVERT: G 376 ASP cc_start: 0.8676 (t0) cc_final: 0.8345 (t0) REVERT: G 414 LEU cc_start: 0.9560 (tt) cc_final: 0.9178 (tt) REVERT: G 471 LYS cc_start: 0.9568 (tptt) cc_final: 0.9355 (tppt) REVERT: G 563 MET cc_start: 0.8728 (tmm) cc_final: 0.8436 (tmm) REVERT: G 565 CYS cc_start: 0.9281 (m) cc_final: 0.8565 (p) REVERT: G 570 MET cc_start: 0.8568 (mtp) cc_final: 0.8253 (mtm) REVERT: G 588 TYR cc_start: 0.9111 (t80) cc_final: 0.8229 (t80) REVERT: G 653 ILE cc_start: 0.9303 (mm) cc_final: 0.9078 (tt) outliers start: 8 outliers final: 0 residues processed: 593 average time/residue: 0.1759 time to fit residues: 154.1895 Evaluate side-chains 265 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 263 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 71] chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 436 ASN B 498 ASN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN C 194 ASN C 368 GLN C 391 GLN C 435 ASN C 605 ASN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 ASN D 202 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 421 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN E 433 GLN E 451 ASN A 749 GLN A 828 ASN A 838 GLN G 284 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044957 restraints weight = 104165.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.046466 restraints weight = 54591.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.047481 restraints weight = 35136.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048178 restraints weight = 25679.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.048592 restraints weight = 20523.963| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 22233 Z= 0.212 Angle : 0.745 11.274 30349 Z= 0.390 Chirality : 0.045 0.265 3503 Planarity : 0.005 0.126 3607 Dihedral : 17.577 74.527 3541 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.07 % Allowed : 13.24 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -0.52 (0.16), residues: 2481 helix: -0.07 (0.12), residues: 1496 sheet: -2.39 (0.29), residues: 219 loop : 0.16 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 135 TYR 0.020 0.002 TYR C 72 PHE 0.028 0.002 PHE C 215 TRP 0.017 0.002 TRP E 276 HIS 0.012 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.21 (22233) covalent geometry : angle 0.74526 / 0.39 (30349) hydrogen bonds : bond 0.05018 / 3.37 ( 1156) hydrogen bonds : angle 4.72254 / 3.36 ( 3312) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 259 time to evaluate : 0.765 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: B 417 MET cc_start: 0.9473 (ttt) cc_final: 0.8659 (tmm) REVERT: B 585 LYS cc_start: 0.9530 (mttt) cc_final: 0.9179 (tmtt) REVERT: C 145 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8946 (mp0) REVERT: C 280 ASP cc_start: 0.8764 (p0) cc_final: 0.8416 (p0) REVERT: C 281 LYS cc_start: 0.9656 (mttm) cc_final: 0.9382 (mtmm) REVERT: C 306 TYR cc_start: 0.9274 (m-80) cc_final: 0.8657 (m-80) REVERT: C 353 MET cc_start: 0.7687 (mmt) cc_final: 0.7244 (mmm) REVERT: C 362 PHE cc_start: 0.9014 (t80) cc_final: 0.8781 (t80) REVERT: C 368 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8929 (pp30) REVERT: C 383 ASP cc_start: 0.9380 (m-30) cc_final: 0.8926 (p0) REVERT: C 389 LEU cc_start: 0.9182 (mt) cc_final: 0.8774 (mt) REVERT: C 402 LEU cc_start: 0.9479 (mt) cc_final: 0.8985 (pp) REVERT: C 571 LEU cc_start: 0.9524 (mm) cc_final: 0.9307 (tp) REVERT: C 625 MET cc_start: 0.8837 (mtp) cc_final: 0.8292 (ttp) REVERT: C 666 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: C 699 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8568 (mt-10) REVERT: D 426 MET cc_start: 0.8888 (mmm) cc_final: 0.8662 (mmm) REVERT: E 1 MET cc_start: 0.7805 (ppp) cc_final: 0.7564 (ppp) REVERT: E 11 LEU cc_start: 0.9607 (mt) cc_final: 0.9388 (tt) REVERT: E 94 ASP cc_start: 0.8379 (t70) cc_final: 0.7942 (t0) REVERT: E 289 GLN cc_start: 0.9348 (tp40) cc_final: 0.8570 (tp-100) REVERT: E 292 MET cc_start: 0.8534 (mpp) cc_final: 0.7171 (mpp) REVERT: E 337 HIS cc_start: 0.8206 (t-90) cc_final: 0.7774 (t-90) REVERT: E 395 GLU cc_start: 0.9180 (tp30) cc_final: 0.8754 (mp0) REVERT: F 232 MET cc_start: 0.9407 (tpp) cc_final: 0.8938 (tpt) REVERT: A 524 MET cc_start: 0.9476 (mmm) cc_final: 0.9121 (mmp) REVERT: A 536 MET cc_start: 0.8840 (tpp) cc_final: 0.7956 (tpp) REVERT: A 716 ILE cc_start: 0.9695 (OUTLIER) cc_final: 0.9375 (tp) REVERT: A 728 MET cc_start: 0.8345 (mmp) cc_final: 0.8124 (mmp) REVERT: A 788 ASP cc_start: 0.9286 (m-30) cc_final: 0.8784 (m-30) REVERT: A 832 MET cc_start: 0.9335 (mmt) cc_final: 0.8890 (mmm) REVERT: A 894 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8347 (mt-10) REVERT: G 327 CYS cc_start: 0.8304 (m) cc_final: 0.8011 (m) REVERT: G 333 VAL cc_start: 0.9005 (t) cc_final: 0.8761 (p) REVERT: G 368 LYS cc_start: 0.8800 (mptt) cc_final: 0.8537 (tppt) REVERT: G 376 ASP cc_start: 0.8256 (t0) cc_final: 0.8050 (t70) REVERT: G 378 ILE cc_start: 0.9286 (tt) cc_final: 0.9060 (tp) REVERT: G 563 MET cc_start: 0.8745 (tmm) cc_final: 0.8491 (tmm) REVERT: G 565 CYS cc_start: 0.9166 (m) cc_final: 0.8855 (p) REVERT: G 588 TYR cc_start: 0.9156 (t80) cc_final: 0.8577 (t80) REVERT: G 610 ASP cc_start: 0.9254 (m-30) cc_final: 0.8969 (m-30) outliers start: 46 outliers final: 24 residues processed: 292 average time/residue: 0.1522 time to fit residues: 69.7757 Evaluate side-chains 226 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 368 GLN Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 716 ILE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 568 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [168, 256, 158, 37, 228, 14, 115, 239, 79, 81, 190] chunk 168 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 115 optimal weight: 0.0060 chunk 239 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 352 ASN B 366 GLN B 577 GLN C 250 HIS ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 GLN ** A 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 585 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.058145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.044928 restraints weight = 103028.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046438 restraints weight = 53450.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047458 restraints weight = 33954.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.048115 restraints weight = 24517.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.048579 restraints weight = 19453.125| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 22233 Z= 0.140 Angle : 0.652 16.095 30349 Z= 0.334 Chirality : 0.043 0.420 3503 Planarity : 0.004 0.086 3607 Dihedral : 17.399 71.372 3537 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.21 % Allowed : 14.14 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.21 (0.17), residues: 2481 helix: 0.67 (0.13), residues: 1491 sheet: -2.13 (0.29), residues: 235 loop : 0.16 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 363 TYR 0.015 0.001 TYR E 258 PHE 0.019 0.001 PHE C 318 TRP 0.016 0.001 TRP E 276 HIS 0.008 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (22233) covalent geometry : angle 0.65201 / 0.33 (30349) hydrogen bonds : bond 0.04387 / 2.97 ( 1156) hydrogen bonds : angle 4.40393 / 3.13 ( 3312) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 0.768 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: B 342 LYS cc_start: 0.9532 (tttt) cc_final: 0.9291 (tptp) REVERT: B 391 LYS cc_start: 0.9336 (tptt) cc_final: 0.8955 (tptt) REVERT: B 417 MET cc_start: 0.9250 (ttt) cc_final: 0.8748 (tmm) REVERT: B 553 MET cc_start: 0.9226 (ttp) cc_final: 0.8857 (ttt) REVERT: B 585 LYS cc_start: 0.9523 (mttt) cc_final: 0.9177 (tmtt) REVERT: C 145 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8731 (pp20) REVERT: C 281 LYS cc_start: 0.9659 (mttm) cc_final: 0.9391 (mtmm) REVERT: C 389 LEU cc_start: 0.9156 (mt) cc_final: 0.8717 (mt) REVERT: C 402 LEU cc_start: 0.9470 (mt) cc_final: 0.8982 (pp) REVERT: C 446 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9224 (tp30) REVERT: C 454 LEU cc_start: 0.8839 (mt) cc_final: 0.8581 (tp) REVERT: C 571 LEU cc_start: 0.9551 (mm) cc_final: 0.9344 (tp) REVERT: C 625 MET cc_start: 0.8897 (mtp) cc_final: 0.8174 (ttp) REVERT: C 699 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8546 (mt-10) REVERT: C 708 MET cc_start: 0.9235 (mmt) cc_final: 0.8931 (mmp) REVERT: D 273 LYS cc_start: 0.9571 (mtpp) cc_final: 0.9352 (mmtm) REVERT: E 1 MET cc_start: 0.7809 (ppp) cc_final: 0.7543 (ppp) REVERT: E 11 LEU cc_start: 0.9606 (mt) cc_final: 0.9387 (tt) REVERT: E 94 ASP cc_start: 0.8348 (t70) cc_final: 0.7896 (t0) REVERT: E 254 CYS cc_start: 0.8866 (m) cc_final: 0.7927 (t) REVERT: E 292 MET cc_start: 0.8589 (mpp) cc_final: 0.8147 (mpp) REVERT: E 337 HIS cc_start: 0.8248 (t-90) cc_final: 0.7839 (t-90) REVERT: E 395 GLU cc_start: 0.9171 (tp30) cc_final: 0.8772 (mp0) REVERT: F 232 MET cc_start: 0.9441 (tpp) cc_final: 0.9019 (tpp) REVERT: A 524 MET cc_start: 0.9470 (mmm) cc_final: 0.9048 (mmp) REVERT: A 536 MET cc_start: 0.8910 (tpp) cc_final: 0.8323 (tpp) REVERT: A 594 MET cc_start: 0.8235 (tpp) cc_final: 0.7896 (tpp) REVERT: A 648 TYR cc_start: 0.9301 (t80) cc_final: 0.9040 (t80) REVERT: A 716 ILE cc_start: 0.9666 (mt) cc_final: 0.9341 (tt) REVERT: A 728 MET cc_start: 0.8375 (mmp) cc_final: 0.8131 (mmp) REVERT: A 788 ASP cc_start: 0.9246 (m-30) cc_final: 0.8887 (t0) REVERT: A 832 MET cc_start: 0.9335 (mmt) cc_final: 0.8885 (mmm) REVERT: A 894 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8435 (mt-10) REVERT: G 324 TYR cc_start: 0.8580 (t80) cc_final: 0.8131 (t80) REVERT: G 327 CYS cc_start: 0.8407 (m) cc_final: 0.7915 (m) REVERT: G 333 VAL cc_start: 0.9034 (t) cc_final: 0.8812 (p) REVERT: G 376 ASP cc_start: 0.8098 (t0) cc_final: 0.7524 (p0) REVERT: G 378 ILE cc_start: 0.9288 (tt) cc_final: 0.9057 (tp) REVERT: G 565 CYS cc_start: 0.9148 (m) cc_final: 0.8835 (p) REVERT: G 588 TYR cc_start: 0.9103 (t80) cc_final: 0.8647 (t80) REVERT: G 610 ASP cc_start: 0.9258 (m-30) cc_final: 0.8934 (m-30) outliers start: 49 outliers final: 23 residues processed: 255 average time/residue: 0.1387 time to fit residues: 56.9696 Evaluate side-chains 207 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [172, 173, 123, 159, 94, 226, 247, 157, 235, 146, 203] chunk 172 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 159 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 235 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 348 ASN ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.057093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.043836 restraints weight = 105566.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045299 restraints weight = 55541.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.046271 restraints weight = 35768.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.046953 restraints weight = 26142.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047379 restraints weight = 20856.795| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22233 Z= 0.188 Angle : 0.652 11.765 30349 Z= 0.336 Chirality : 0.043 0.427 3503 Planarity : 0.004 0.064 3607 Dihedral : 17.364 69.905 3537 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer: Outliers : 2.34 % Allowed : 15.05 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.64 (0.17), residues: 2481 helix: 1.11 (0.13), residues: 1502 sheet: -1.88 (0.31), residues: 223 loop : 0.02 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 575 TYR 0.016 0.001 TYR E 258 PHE 0.036 0.002 PHE C 362 TRP 0.008 0.001 TRP C 191 HIS 0.009 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (22233) covalent geometry : angle 0.65204 / 0.34 (30349) hydrogen bonds : bond 0.04211 / 2.84 ( 1156) hydrogen bonds : angle 4.32303 / 3.06 ( 3312) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 0.781 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 342 LYS cc_start: 0.9536 (tttt) cc_final: 0.9282 (tptp) REVERT: B 417 MET cc_start: 0.9290 (ttt) cc_final: 0.8744 (tmm) REVERT: B 553 MET cc_start: 0.9249 (ttp) cc_final: 0.8881 (ttt) REVERT: B 585 LYS cc_start: 0.9514 (mttt) cc_final: 0.9205 (tmtt) REVERT: C 145 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8744 (pp20) REVERT: C 281 LYS cc_start: 0.9644 (mttm) cc_final: 0.9393 (mtmm) REVERT: C 306 TYR cc_start: 0.9275 (m-80) cc_final: 0.8977 (m-80) REVERT: C 389 LEU cc_start: 0.9222 (mt) cc_final: 0.8775 (mt) REVERT: C 402 LEU cc_start: 0.9510 (mt) cc_final: 0.9088 (pp) REVERT: C 446 GLU cc_start: 0.9488 (mt-10) cc_final: 0.9211 (tp30) REVERT: C 454 LEU cc_start: 0.8913 (mt) cc_final: 0.8673 (tp) REVERT: C 571 LEU cc_start: 0.9569 (mm) cc_final: 0.9362 (tp) REVERT: C 666 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: C 699 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8529 (mt-10) REVERT: C 708 MET cc_start: 0.9231 (mmt) cc_final: 0.8932 (mmp) REVERT: E 1 MET cc_start: 0.7867 (ppp) cc_final: 0.7660 (ppp) REVERT: E 11 LEU cc_start: 0.9591 (mt) cc_final: 0.9362 (tt) REVERT: E 94 ASP cc_start: 0.8372 (t70) cc_final: 0.7922 (t0) REVERT: E 254 CYS cc_start: 0.8901 (m) cc_final: 0.8015 (t) REVERT: E 292 MET cc_start: 0.8650 (mpp) cc_final: 0.8105 (mpp) REVERT: E 395 GLU cc_start: 0.9172 (tp30) cc_final: 0.8719 (mm-30) REVERT: F 232 MET cc_start: 0.9504 (tpp) cc_final: 0.9126 (tpt) REVERT: F 233 LEU cc_start: 0.9323 (pp) cc_final: 0.9075 (pp) REVERT: A 524 MET cc_start: 0.9458 (mmm) cc_final: 0.8930 (mmp) REVERT: A 536 MET cc_start: 0.8876 (tpp) cc_final: 0.8281 (tpp) REVERT: A 594 MET cc_start: 0.8321 (tpp) cc_final: 0.8066 (tpp) REVERT: A 716 ILE cc_start: 0.9665 (mt) cc_final: 0.9296 (tp) REVERT: A 728 MET cc_start: 0.8418 (mmp) cc_final: 0.8092 (mmm) REVERT: A 788 ASP cc_start: 0.9199 (m-30) cc_final: 0.8735 (m-30) REVERT: A 832 MET cc_start: 0.9345 (mmt) cc_final: 0.8930 (mmm) REVERT: A 894 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8417 (mt-10) REVERT: G 324 TYR cc_start: 0.8655 (t80) cc_final: 0.8059 (t80) REVERT: G 327 CYS cc_start: 0.8382 (m) cc_final: 0.7862 (m) REVERT: G 333 VAL cc_start: 0.9052 (t) cc_final: 0.8812 (p) REVERT: G 376 ASP cc_start: 0.8145 (t0) cc_final: 0.7452 (p0) REVERT: G 378 ILE cc_start: 0.9337 (tt) cc_final: 0.9110 (tp) REVERT: G 563 MET cc_start: 0.8677 (tmm) cc_final: 0.8465 (tmm) REVERT: G 588 TYR cc_start: 0.9096 (t80) cc_final: 0.8739 (t80) REVERT: G 610 ASP cc_start: 0.9265 (m-30) cc_final: 0.8941 (m-30) outliers start: 52 outliers final: 29 residues processed: 235 average time/residue: 0.1506 time to fit residues: 56.1015 Evaluate side-chains 204 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 411 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 463 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [21, 208, 193, 148, 31, 2, 32, 207, 181, 62, 170] chunk 21 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 325 HIS ** C 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.044180 restraints weight = 105135.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.045637 restraints weight = 56074.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046624 restraints weight = 36364.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.047264 restraints weight = 26831.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047720 restraints weight = 21699.568| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22233 Z= 0.133 Angle : 0.602 10.894 30349 Z= 0.309 Chirality : 0.041 0.358 3503 Planarity : 0.004 0.057 3607 Dihedral : 17.300 69.255 3537 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 2.16 % Allowed : 16.44 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 0.85 (0.17), residues: 2481 helix: 1.33 (0.14), residues: 1502 sheet: -1.75 (0.31), residues: 234 loop : -0.02 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 426 TYR 0.026 0.001 TYR C 72 PHE 0.019 0.001 PHE C 318 TRP 0.012 0.001 TRP D 271 HIS 0.007 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22233) covalent geometry : angle 0.60212 / 0.31 (30349) hydrogen bonds : bond 0.03867 / 2.64 ( 1156) hydrogen bonds : angle 4.14489 / 2.93 ( 3312) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 203 time to evaluate : 0.740 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 342 LYS cc_start: 0.9515 (tttt) cc_final: 0.9264 (tptp) REVERT: B 391 LYS cc_start: 0.9255 (tptt) cc_final: 0.8867 (tppt) REVERT: B 417 MET cc_start: 0.9267 (ttt) cc_final: 0.8757 (tmm) REVERT: B 585 LYS cc_start: 0.9506 (mttt) cc_final: 0.9213 (tmtt) REVERT: B 610 GLN cc_start: 0.8939 (mt0) cc_final: 0.8737 (mp10) REVERT: C 145 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8787 (pp20) REVERT: C 281 LYS cc_start: 0.9634 (mttm) cc_final: 0.9384 (mtmm) REVERT: C 306 TYR cc_start: 0.9246 (m-80) cc_final: 0.8521 (m-80) REVERT: C 389 LEU cc_start: 0.9203 (mt) cc_final: 0.8773 (mt) REVERT: C 402 LEU cc_start: 0.9494 (mt) cc_final: 0.9068 (pp) REVERT: C 426 ARG cc_start: 0.8648 (mmt90) cc_final: 0.8245 (mmt90) REVERT: C 446 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9223 (tp30) REVERT: C 454 LEU cc_start: 0.8940 (mt) cc_final: 0.8695 (tp) REVERT: C 495 LEU cc_start: 0.9454 (mm) cc_final: 0.8892 (tt) REVERT: C 571 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9379 (tp) REVERT: C 592 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: C 699 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8561 (mp0) REVERT: C 708 MET cc_start: 0.9210 (mmt) cc_final: 0.8937 (mmm) REVERT: E 1 MET cc_start: 0.7872 (ppp) cc_final: 0.7639 (ppp) REVERT: E 11 LEU cc_start: 0.9579 (mt) cc_final: 0.9331 (tt) REVERT: E 94 ASP cc_start: 0.8374 (t70) cc_final: 0.7910 (t0) REVERT: E 254 CYS cc_start: 0.8888 (m) cc_final: 0.8021 (t) REVERT: E 292 MET cc_start: 0.8714 (mpp) cc_final: 0.8198 (mpp) REVERT: E 395 GLU cc_start: 0.9135 (tp30) cc_final: 0.8750 (mp0) REVERT: F 232 MET cc_start: 0.9430 (tpp) cc_final: 0.9119 (tpt) REVERT: A 524 MET cc_start: 0.9460 (mmm) cc_final: 0.8919 (mmp) REVERT: A 536 MET cc_start: 0.8881 (tpp) cc_final: 0.8270 (tpp) REVERT: A 594 MET cc_start: 0.8333 (tpp) cc_final: 0.8094 (tpp) REVERT: A 728 MET cc_start: 0.8416 (mmp) cc_final: 0.8075 (mmm) REVERT: A 788 ASP cc_start: 0.9149 (m-30) cc_final: 0.8676 (m-30) REVERT: A 832 MET cc_start: 0.9324 (mmt) cc_final: 0.8927 (mmm) REVERT: G 324 TYR cc_start: 0.8661 (t80) cc_final: 0.7981 (t80) REVERT: G 327 CYS cc_start: 0.8361 (m) cc_final: 0.7822 (m) REVERT: G 333 VAL cc_start: 0.9083 (t) cc_final: 0.8829 (p) REVERT: G 376 ASP cc_start: 0.8177 (t0) cc_final: 0.7308 (p0) REVERT: G 378 ILE cc_start: 0.9346 (tt) cc_final: 0.9117 (tp) REVERT: G 420 MET cc_start: 0.9186 (pmm) cc_final: 0.8800 (pmm) REVERT: G 565 CYS cc_start: 0.9195 (m) cc_final: 0.8928 (p) REVERT: G 588 TYR cc_start: 0.9083 (t80) cc_final: 0.8716 (t80) REVERT: G 610 ASP cc_start: 0.9250 (m-30) cc_final: 0.8930 (m-30) outliers start: 48 outliers final: 30 residues processed: 242 average time/residue: 0.1329 time to fit residues: 52.2676 Evaluate side-chains 204 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 592 GLU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 666 GLN Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 882 CYS Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [66, 176, 21, 10, 77, 12, 82, 205, 125, 168, 108] chunk 66 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 609 GLN C 666 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN G 576 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.058999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.045952 restraints weight = 104740.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.047428 restraints weight = 54340.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.048429 restraints weight = 34471.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.049095 restraints weight = 24860.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.049542 restraints weight = 19778.776| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22233 Z= 0.114 Angle : 0.596 11.932 30349 Z= 0.304 Chirality : 0.040 0.371 3503 Planarity : 0.004 0.052 3607 Dihedral : 17.160 68.474 3537 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.94 % Allowed : 16.98 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.02 (0.17), residues: 2481 helix: 1.45 (0.14), residues: 1503 sheet: -1.56 (0.31), residues: 234 loop : 0.03 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.041 0.001 TYR C 72 PHE 0.019 0.001 PHE C 318 TRP 0.009 0.001 TRP E 276 HIS 0.010 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (22233) covalent geometry : angle 0.59623 / 0.30 (30349) hydrogen bonds : bond 0.03664 / 2.50 ( 1156) hydrogen bonds : angle 4.04547 / 2.87 ( 3312) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.805 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 417 MET cc_start: 0.9257 (ttt) cc_final: 0.8938 (tmm) REVERT: B 540 TYR cc_start: 0.8528 (t80) cc_final: 0.8294 (t80) REVERT: B 585 LYS cc_start: 0.9501 (mttt) cc_final: 0.9220 (tmtt) REVERT: C 145 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8795 (pp20) REVERT: C 281 LYS cc_start: 0.9597 (mttm) cc_final: 0.9342 (mtmm) REVERT: C 389 LEU cc_start: 0.9191 (mt) cc_final: 0.8754 (mt) REVERT: C 426 ARG cc_start: 0.8747 (mmt90) cc_final: 0.8327 (mmt90) REVERT: C 446 GLU cc_start: 0.9504 (mt-10) cc_final: 0.9053 (tp30) REVERT: C 450 MET cc_start: 0.8463 (mtp) cc_final: 0.6621 (mtp) REVERT: C 454 LEU cc_start: 0.8953 (mt) cc_final: 0.8700 (tp) REVERT: C 495 LEU cc_start: 0.9452 (mm) cc_final: 0.8922 (tt) REVERT: C 571 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9348 (tp) REVERT: C 699 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8577 (mp0) REVERT: C 708 MET cc_start: 0.9190 (mmt) cc_final: 0.8885 (mmp) REVERT: D 347 GLU cc_start: 0.8984 (mp0) cc_final: 0.8646 (mp0) REVERT: E 11 LEU cc_start: 0.9577 (mt) cc_final: 0.9321 (tt) REVERT: E 94 ASP cc_start: 0.8324 (t70) cc_final: 0.7850 (t0) REVERT: E 254 CYS cc_start: 0.8860 (m) cc_final: 0.8037 (t) REVERT: E 292 MET cc_start: 0.8667 (mpp) cc_final: 0.8116 (mpp) REVERT: E 395 GLU cc_start: 0.9121 (tp30) cc_final: 0.8758 (mp0) REVERT: F 232 MET cc_start: 0.9471 (tpp) cc_final: 0.9187 (tpt) REVERT: A 524 MET cc_start: 0.9456 (mmm) cc_final: 0.8902 (mmp) REVERT: A 536 MET cc_start: 0.8897 (tpp) cc_final: 0.8272 (tpp) REVERT: A 594 MET cc_start: 0.8359 (tpp) cc_final: 0.8098 (tpp) REVERT: A 728 MET cc_start: 0.8389 (mmp) cc_final: 0.8059 (mmm) REVERT: A 788 ASP cc_start: 0.9186 (m-30) cc_final: 0.8717 (m-30) REVERT: A 805 VAL cc_start: 0.8880 (t) cc_final: 0.8555 (t) REVERT: A 832 MET cc_start: 0.9329 (mmt) cc_final: 0.8926 (mmm) REVERT: G 324 TYR cc_start: 0.8684 (t80) cc_final: 0.7989 (t80) REVERT: G 327 CYS cc_start: 0.8292 (m) cc_final: 0.7738 (m) REVERT: G 333 VAL cc_start: 0.9140 (t) cc_final: 0.8892 (p) REVERT: G 376 ASP cc_start: 0.8082 (t0) cc_final: 0.7366 (p0) REVERT: G 378 ILE cc_start: 0.9335 (tt) cc_final: 0.9097 (tp) REVERT: G 420 MET cc_start: 0.9218 (pmm) cc_final: 0.8763 (pmm) REVERT: G 565 CYS cc_start: 0.9193 (m) cc_final: 0.8966 (p) REVERT: G 588 TYR cc_start: 0.9056 (t80) cc_final: 0.8724 (t80) REVERT: G 610 ASP cc_start: 0.9257 (m-30) cc_final: 0.8929 (m-30) outliers start: 43 outliers final: 26 residues processed: 225 average time/residue: 0.1326 time to fit residues: 49.1903 Evaluate side-chains 200 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [115, 217, 143, 209, 158, 56, 109, 157, 25, 49, 41] chunk 115 optimal weight: 0.0980 chunk 217 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 113 GLN C 575 GLN ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN A 749 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.058287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044605 restraints weight = 105358.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.046077 restraints weight = 55809.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.047057 restraints weight = 36150.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047704 restraints weight = 26652.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.048156 restraints weight = 21517.676| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22233 Z= 0.119 Angle : 0.598 12.754 30349 Z= 0.303 Chirality : 0.041 0.395 3503 Planarity : 0.003 0.045 3607 Dihedral : 17.050 67.949 3537 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.98 % Allowed : 17.66 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.10 (0.17), residues: 2481 helix: 1.52 (0.14), residues: 1502 sheet: -1.50 (0.31), residues: 245 loop : 0.06 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 575 TYR 0.047 0.001 TYR C 72 PHE 0.017 0.001 PHE C 318 TRP 0.009 0.001 TRP E 276 HIS 0.006 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22233) covalent geometry : angle 0.59819 / 0.30 (30349) hydrogen bonds : bond 0.03590 / 2.45 ( 1156) hydrogen bonds : angle 4.02400 / 2.85 ( 3312) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 183 time to evaluate : 0.838 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 417 MET cc_start: 0.9257 (ttt) cc_final: 0.8845 (tmm) REVERT: B 585 LYS cc_start: 0.9501 (mttt) cc_final: 0.9221 (tmtt) REVERT: C 145 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8812 (pp20) REVERT: C 281 LYS cc_start: 0.9595 (mttm) cc_final: 0.9351 (mtmm) REVERT: C 306 TYR cc_start: 0.9220 (m-80) cc_final: 0.8522 (m-80) REVERT: C 389 LEU cc_start: 0.9203 (mt) cc_final: 0.8765 (mt) REVERT: C 426 ARG cc_start: 0.8860 (mmt90) cc_final: 0.8438 (mmt90) REVERT: C 446 GLU cc_start: 0.9517 (mt-10) cc_final: 0.9090 (tp30) REVERT: C 450 MET cc_start: 0.8514 (mtp) cc_final: 0.6711 (mtp) REVERT: C 454 LEU cc_start: 0.8951 (mt) cc_final: 0.8698 (tp) REVERT: C 495 LEU cc_start: 0.9507 (mm) cc_final: 0.8938 (tt) REVERT: C 699 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8588 (mp0) REVERT: C 708 MET cc_start: 0.9179 (mmt) cc_final: 0.8937 (mmm) REVERT: D 347 GLU cc_start: 0.8962 (mp0) cc_final: 0.8644 (mp0) REVERT: E 11 LEU cc_start: 0.9576 (mt) cc_final: 0.9321 (tt) REVERT: E 80 MET cc_start: 0.8992 (ptp) cc_final: 0.8636 (ptp) REVERT: E 94 ASP cc_start: 0.8400 (t70) cc_final: 0.7930 (t0) REVERT: E 254 CYS cc_start: 0.8860 (m) cc_final: 0.8052 (t) REVERT: E 292 MET cc_start: 0.8664 (mpp) cc_final: 0.8091 (mpp) REVERT: E 395 GLU cc_start: 0.9125 (tp30) cc_final: 0.8741 (mp0) REVERT: F 232 MET cc_start: 0.9491 (tpp) cc_final: 0.9220 (tpt) REVERT: A 524 MET cc_start: 0.9463 (mmm) cc_final: 0.8884 (mmp) REVERT: A 536 MET cc_start: 0.8902 (tpp) cc_final: 0.8273 (tpp) REVERT: A 728 MET cc_start: 0.8386 (mmp) cc_final: 0.8055 (mmm) REVERT: A 788 ASP cc_start: 0.9177 (m-30) cc_final: 0.8705 (m-30) REVERT: A 805 VAL cc_start: 0.8879 (t) cc_final: 0.8548 (t) REVERT: A 832 MET cc_start: 0.9318 (mmt) cc_final: 0.8895 (mmm) REVERT: G 324 TYR cc_start: 0.8725 (t80) cc_final: 0.8017 (t80) REVERT: G 327 CYS cc_start: 0.8325 (m) cc_final: 0.7804 (m) REVERT: G 333 VAL cc_start: 0.9161 (t) cc_final: 0.8921 (p) REVERT: G 370 MET cc_start: 0.8850 (tpp) cc_final: 0.8644 (tpp) REVERT: G 376 ASP cc_start: 0.8136 (t0) cc_final: 0.7366 (p0) REVERT: G 378 ILE cc_start: 0.9337 (tt) cc_final: 0.9094 (tp) REVERT: G 420 MET cc_start: 0.9231 (pmm) cc_final: 0.8745 (pmm) REVERT: G 565 CYS cc_start: 0.9148 (m) cc_final: 0.8920 (p) REVERT: G 588 TYR cc_start: 0.9030 (t80) cc_final: 0.8724 (t80) REVERT: G 610 ASP cc_start: 0.9273 (m-30) cc_final: 0.8957 (m-30) outliers start: 44 outliers final: 30 residues processed: 219 average time/residue: 0.1272 time to fit residues: 46.5401 Evaluate side-chains 202 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [220, 82, 225, 69, 137, 162, 34, 214, 63, 207, 216] chunk 220 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 214 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 216 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 609 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.057610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.044746 restraints weight = 105762.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046155 restraints weight = 55167.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.047082 restraints weight = 35326.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.047676 restraints weight = 25819.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.048113 restraints weight = 20826.946| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22233 Z= 0.159 Angle : 0.623 14.608 30349 Z= 0.315 Chirality : 0.041 0.355 3503 Planarity : 0.004 0.046 3607 Dihedral : 16.988 68.871 3537 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.94 % Allowed : 18.15 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.22 (0.17), residues: 2481 helix: 1.67 (0.14), residues: 1499 sheet: -1.53 (0.30), residues: 252 loop : 0.04 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 575 TYR 0.014 0.001 TYR C 306 PHE 0.015 0.001 PHE G 280 TRP 0.013 0.001 TRP B 343 HIS 0.008 0.001 HIS C 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (22233) covalent geometry : angle 0.62306 / 0.32 (30349) hydrogen bonds : bond 0.03685 / 2.51 ( 1156) hydrogen bonds : angle 4.02168 / 2.85 ( 3312) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 173 time to evaluate : 0.716 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 417 MET cc_start: 0.9266 (ttt) cc_final: 0.8865 (tmm) REVERT: B 585 LYS cc_start: 0.9487 (mttt) cc_final: 0.9182 (tmtt) REVERT: C 145 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.8875 (pp20) REVERT: C 281 LYS cc_start: 0.9577 (mttm) cc_final: 0.9326 (mtmm) REVERT: C 306 TYR cc_start: 0.9276 (m-80) cc_final: 0.9069 (m-80) REVERT: C 389 LEU cc_start: 0.9244 (mt) cc_final: 0.8822 (mt) REVERT: C 426 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8646 (mmt90) REVERT: C 446 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9227 (tp30) REVERT: C 450 MET cc_start: 0.8524 (mtp) cc_final: 0.6600 (mtp) REVERT: C 451 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8524 (pp) REVERT: C 495 LEU cc_start: 0.9503 (mm) cc_final: 0.8934 (tt) REVERT: C 699 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8693 (mp0) REVERT: C 708 MET cc_start: 0.9149 (mmt) cc_final: 0.8905 (mmm) REVERT: D 347 GLU cc_start: 0.8995 (mp0) cc_final: 0.8673 (mp0) REVERT: E 11 LEU cc_start: 0.9591 (mt) cc_final: 0.9310 (tt) REVERT: E 80 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8703 (ptp) REVERT: E 94 ASP cc_start: 0.8361 (t70) cc_final: 0.7880 (t0) REVERT: E 254 CYS cc_start: 0.8902 (m) cc_final: 0.8109 (t) REVERT: E 292 MET cc_start: 0.8607 (mpp) cc_final: 0.8063 (mpp) REVERT: E 395 GLU cc_start: 0.9146 (tp30) cc_final: 0.8671 (mm-30) REVERT: F 232 MET cc_start: 0.9534 (tpp) cc_final: 0.9281 (tpt) REVERT: A 524 MET cc_start: 0.9454 (mmm) cc_final: 0.8848 (mmp) REVERT: A 536 MET cc_start: 0.8960 (tpp) cc_final: 0.8283 (tpp) REVERT: A 728 MET cc_start: 0.8416 (mmp) cc_final: 0.8071 (mmm) REVERT: A 788 ASP cc_start: 0.9181 (m-30) cc_final: 0.8719 (m-30) REVERT: A 805 VAL cc_start: 0.8891 (t) cc_final: 0.8551 (t) REVERT: A 832 MET cc_start: 0.9319 (mmt) cc_final: 0.8916 (mmm) REVERT: G 324 TYR cc_start: 0.8762 (t80) cc_final: 0.8008 (t80) REVERT: G 327 CYS cc_start: 0.8414 (m) cc_final: 0.7864 (m) REVERT: G 333 VAL cc_start: 0.9199 (t) cc_final: 0.8963 (p) REVERT: G 370 MET cc_start: 0.8875 (tpp) cc_final: 0.8367 (tpp) REVERT: G 376 ASP cc_start: 0.8103 (t0) cc_final: 0.7184 (p0) REVERT: G 378 ILE cc_start: 0.9368 (tt) cc_final: 0.9119 (tp) REVERT: G 420 MET cc_start: 0.9237 (pmm) cc_final: 0.8738 (pmm) REVERT: G 565 CYS cc_start: 0.9142 (m) cc_final: 0.8922 (p) REVERT: G 581 MET cc_start: 0.9165 (mmm) cc_final: 0.8712 (tpp) REVERT: G 588 TYR cc_start: 0.9042 (t80) cc_final: 0.8792 (t80) REVERT: G 610 ASP cc_start: 0.9270 (m-30) cc_final: 0.8965 (m-30) outliers start: 43 outliers final: 34 residues processed: 210 average time/residue: 0.1375 time to fit residues: 47.6353 Evaluate side-chains 194 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 338 LYS Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [223, 124, 2, 222, 128, 102, 175, 236, 104, 253, 203] chunk 223 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 222 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 253 optimal weight: 50.0000 chunk 203 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 609 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS E 150 ASN E 414 ASN F 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.057703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.044505 restraints weight = 104299.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045958 restraints weight = 54882.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.046932 restraints weight = 35238.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.047557 restraints weight = 25664.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.048037 restraints weight = 20633.348| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22233 Z= 0.112 Angle : 0.618 14.862 30349 Z= 0.307 Chirality : 0.041 0.369 3503 Planarity : 0.003 0.047 3607 Dihedral : 16.915 69.754 3537 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.98 % Allowed : 18.06 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.27 (0.17), residues: 2481 helix: 1.67 (0.14), residues: 1493 sheet: -1.44 (0.30), residues: 252 loop : 0.13 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 575 TYR 0.037 0.001 TYR C 72 PHE 0.016 0.001 PHE C 318 TRP 0.025 0.001 TRP B 343 HIS 0.006 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (22233) covalent geometry : angle 0.61787 / 0.31 (30349) hydrogen bonds : bond 0.03459 / 2.38 ( 1156) hydrogen bonds : angle 3.95267 / 2.80 ( 3312) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 175 time to evaluate : 0.892 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 417 MET cc_start: 0.9307 (ttt) cc_final: 0.8969 (tmm) REVERT: B 585 LYS cc_start: 0.9488 (mttt) cc_final: 0.9177 (tmtt) REVERT: C 145 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8896 (pp20) REVERT: C 281 LYS cc_start: 0.9562 (mttm) cc_final: 0.9318 (mtmm) REVERT: C 306 TYR cc_start: 0.9232 (m-80) cc_final: 0.8526 (m-80) REVERT: C 389 LEU cc_start: 0.9199 (mt) cc_final: 0.8781 (mt) REVERT: C 426 ARG cc_start: 0.8932 (mmt90) cc_final: 0.8629 (mmt90) REVERT: C 446 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9204 (tp30) REVERT: C 450 MET cc_start: 0.8526 (mtp) cc_final: 0.6595 (mtp) REVERT: C 495 LEU cc_start: 0.9478 (mm) cc_final: 0.9015 (tt) REVERT: C 699 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8687 (mp0) REVERT: C 708 MET cc_start: 0.9138 (mmt) cc_final: 0.8903 (mmm) REVERT: D 347 GLU cc_start: 0.8992 (mp0) cc_final: 0.8655 (mp0) REVERT: E 11 LEU cc_start: 0.9586 (mt) cc_final: 0.9311 (tt) REVERT: E 80 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8679 (ptp) REVERT: E 94 ASP cc_start: 0.8391 (t70) cc_final: 0.7910 (t0) REVERT: E 254 CYS cc_start: 0.8883 (m) cc_final: 0.8102 (t) REVERT: E 292 MET cc_start: 0.8552 (mpp) cc_final: 0.7979 (mpp) REVERT: E 395 GLU cc_start: 0.9104 (tp30) cc_final: 0.8745 (mp0) REVERT: E 440 PHE cc_start: 0.8807 (t80) cc_final: 0.8438 (t80) REVERT: F 232 MET cc_start: 0.9532 (tpp) cc_final: 0.9275 (tpt) REVERT: A 524 MET cc_start: 0.9454 (mmm) cc_final: 0.8843 (mmp) REVERT: A 536 MET cc_start: 0.8950 (tpp) cc_final: 0.8277 (tpp) REVERT: A 728 MET cc_start: 0.8403 (mmp) cc_final: 0.8086 (mmm) REVERT: A 788 ASP cc_start: 0.9190 (m-30) cc_final: 0.8697 (m-30) REVERT: A 805 VAL cc_start: 0.8837 (t) cc_final: 0.8502 (t) REVERT: A 832 MET cc_start: 0.9307 (mmt) cc_final: 0.8900 (mmm) REVERT: G 324 TYR cc_start: 0.8710 (t80) cc_final: 0.7945 (t80) REVERT: G 327 CYS cc_start: 0.8350 (m) cc_final: 0.7779 (m) REVERT: G 333 VAL cc_start: 0.9192 (t) cc_final: 0.8948 (p) REVERT: G 370 MET cc_start: 0.8885 (tpp) cc_final: 0.8648 (tpp) REVERT: G 376 ASP cc_start: 0.7875 (t0) cc_final: 0.7123 (p0) REVERT: G 378 ILE cc_start: 0.9336 (tt) cc_final: 0.9084 (tp) REVERT: G 420 MET cc_start: 0.9219 (pmm) cc_final: 0.8727 (pmm) REVERT: G 565 CYS cc_start: 0.9143 (m) cc_final: 0.8916 (p) REVERT: G 581 MET cc_start: 0.9155 (mmm) cc_final: 0.8693 (tpp) REVERT: G 588 TYR cc_start: 0.8992 (t80) cc_final: 0.8735 (t80) REVERT: G 610 ASP cc_start: 0.9258 (m-30) cc_final: 0.8949 (m-30) outliers start: 44 outliers final: 34 residues processed: 209 average time/residue: 0.1281 time to fit residues: 44.7814 Evaluate side-chains 200 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [252, 126, 36, 65, 32, 174, 160, 11, 47, 173, 24] chunk 252 optimal weight: 30.0000 chunk 126 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 160 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 609 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.057587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.044375 restraints weight = 104739.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045852 restraints weight = 54934.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046819 restraints weight = 35215.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.047453 restraints weight = 25688.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.047922 restraints weight = 20647.855| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22233 Z= 0.118 Angle : 0.623 14.834 30349 Z= 0.308 Chirality : 0.041 0.365 3503 Planarity : 0.003 0.045 3607 Dihedral : 16.858 71.221 3537 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.80 % Allowed : 18.51 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.33 (0.17), residues: 2481 helix: 1.70 (0.14), residues: 1500 sheet: -1.38 (0.30), residues: 252 loop : 0.16 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 575 TYR 0.071 0.001 TYR C 72 PHE 0.015 0.001 PHE C 318 TRP 0.019 0.001 TRP B 343 HIS 0.006 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22233) covalent geometry : angle 0.62258 / 0.31 (30349) hydrogen bonds : bond 0.03456 / 2.38 ( 1156) hydrogen bonds : angle 3.95816 / 2.80 ( 3312) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4962 Ramachandran restraints generated. 2481 Oldfield, 0 Emsley, 2481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.653 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 417 MET cc_start: 0.9307 (ttt) cc_final: 0.8967 (tmm) REVERT: B 585 LYS cc_start: 0.9491 (mttt) cc_final: 0.9192 (tmtt) REVERT: C 145 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8893 (pp20) REVERT: C 281 LYS cc_start: 0.9547 (mttm) cc_final: 0.9294 (mtmm) REVERT: C 306 TYR cc_start: 0.9239 (m-80) cc_final: 0.8541 (m-80) REVERT: C 389 LEU cc_start: 0.9212 (mt) cc_final: 0.8794 (mt) REVERT: C 426 ARG cc_start: 0.8992 (mmt90) cc_final: 0.8659 (mmt90) REVERT: C 446 GLU cc_start: 0.9530 (mt-10) cc_final: 0.9066 (tp30) REVERT: C 450 MET cc_start: 0.8509 (mtp) cc_final: 0.6609 (mtp) REVERT: C 451 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 454 LEU cc_start: 0.8691 (tp) cc_final: 0.8465 (tt) REVERT: C 495 LEU cc_start: 0.9522 (mm) cc_final: 0.9011 (tt) REVERT: C 699 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8717 (mp0) REVERT: C 708 MET cc_start: 0.9138 (mmt) cc_final: 0.8889 (mmm) REVERT: D 347 GLU cc_start: 0.9019 (mp0) cc_final: 0.8685 (mp0) REVERT: E 1 MET cc_start: 0.8010 (ppp) cc_final: 0.7315 (ppp) REVERT: E 11 LEU cc_start: 0.9594 (mt) cc_final: 0.9314 (tt) REVERT: E 80 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8727 (ptp) REVERT: E 94 ASP cc_start: 0.8395 (t70) cc_final: 0.7924 (t0) REVERT: E 254 CYS cc_start: 0.8898 (m) cc_final: 0.8121 (t) REVERT: E 292 MET cc_start: 0.8513 (mpp) cc_final: 0.7934 (mpp) REVERT: E 440 PHE cc_start: 0.8815 (t80) cc_final: 0.8515 (t80) REVERT: F 232 MET cc_start: 0.9554 (tpp) cc_final: 0.9308 (tpt) REVERT: A 524 MET cc_start: 0.9457 (mmm) cc_final: 0.8837 (mmp) REVERT: A 536 MET cc_start: 0.8959 (tpp) cc_final: 0.8284 (tpp) REVERT: A 728 MET cc_start: 0.8398 (mmp) cc_final: 0.8087 (mmm) REVERT: A 788 ASP cc_start: 0.9186 (m-30) cc_final: 0.8757 (t0) REVERT: A 805 VAL cc_start: 0.8841 (t) cc_final: 0.8509 (t) REVERT: A 832 MET cc_start: 0.9310 (mmt) cc_final: 0.8886 (mmm) REVERT: G 324 TYR cc_start: 0.8705 (t80) cc_final: 0.7997 (t80) REVERT: G 327 CYS cc_start: 0.8315 (m) cc_final: 0.7767 (m) REVERT: G 333 VAL cc_start: 0.9186 (t) cc_final: 0.8950 (p) REVERT: G 370 MET cc_start: 0.8896 (tpp) cc_final: 0.8658 (tpp) REVERT: G 376 ASP cc_start: 0.8045 (t0) cc_final: 0.7219 (p0) REVERT: G 378 ILE cc_start: 0.9335 (tt) cc_final: 0.9064 (tp) REVERT: G 420 MET cc_start: 0.9226 (pmm) cc_final: 0.8750 (pmm) REVERT: G 565 CYS cc_start: 0.9164 (m) cc_final: 0.8924 (p) REVERT: G 581 MET cc_start: 0.9160 (mmm) cc_final: 0.8711 (tpp) REVERT: G 610 ASP cc_start: 0.9260 (m-30) cc_final: 0.8952 (m-30) outliers start: 40 outliers final: 33 residues processed: 204 average time/residue: 0.1305 time to fit residues: 44.2213 Evaluate side-chains 198 residues out of total 2221 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain A residue 764 PHE Chi-restraints excluded: chain A residue 804 CYS Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 352 THR Chi-restraints excluded: chain G residue 403 ILE Chi-restraints excluded: chain G residue 463 VAL Chi-restraints excluded: chain G residue 657 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: [158, 156, 117, 16, 228, 238, 113, 13, 224, 243, 172] chunk 158 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 243 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 609 GLN ** D 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 399 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 = 0.3253 r_free = 0.3253 target = 0.057627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.044442 restraints weight = 105215.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045890 restraints weight = 55395.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046854 restraints weight = 35681.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.047484 restraints weight = 26087.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047957 restraints weight = 20990.234| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.181 22233 Z= 0.154 Angle : 0.754 59.198 30349 Z= 0.410 Chirality : 0.041 0.379 3503 Planarity : 0.003 0.045 3607 Dihedral : 16.858 71.230 3537 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.76 % Allowed : 18.69 % Favored : 79.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: 1.32 (0.17), residues: 2481 helix: 1.69 (0.14), residues: 1500 sheet: -1.37 (0.30), residues: 252 loop : 0.16 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 575 TYR 0.055 0.001 TYR C 72 PHE 0.019 0.001 PHE A 867 TRP 0.016 0.001 TRP B 343 HIS 0.005 0.001 HIS G 641 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (22233) covalent geometry : angle 0.75443 / 0.41 (30349) hydrogen bonds : bond 0.03463 / 2.38 ( 1156) hydrogen bonds : angle 3.95738 / 2.80 ( 3312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3146.79 seconds wall clock time: 55 minutes 26.23 seconds (3326.23 seconds total)